===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
fsl-5.0.8/doc/fsl/fsl_installer.sh-112- the_profile=$1
fsl-5.0.8/doc/fsl/fsl_installer.sh:113: if [ `echo ${the_profile} | grep 'csh'` ] ; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-114- echo 1
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-119- the_profile=$1
fsl-5.0.8/doc/fsl/fsl_installer.sh:120: if [ `echo ${the_profile} | grep 'profile'` ] ; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-121- echo 1
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-127- user_profile=$2
fsl-5.0.8/doc/fsl/fsl_installer.sh:128: if [ `is_sh ${user_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-129- search_string='FSLDIR='
fsl-5.0.8/doc/fsl/fsl_installer.sh:130: elif [ `is_csh ${user_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-131- search_string='setenv FSLDIR '
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-198- user_profile=$2
fsl-5.0.8/doc/fsl/fsl_installer.sh:199: if [ `is_csh ${user_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-200- fsl_csh ${user_profile} ${fsldir} 0
fsl-5.0.8/doc/fsl/fsl_installer.sh:201: elif [ `is_sh ${user_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-202- fsl_sh ${user_profile} ${fsldir} 0
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-214- display_profile=$1
fsl-5.0.8/doc/fsl/fsl_installer.sh:215: if [ `is_sh ${display_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-216- remove='if \[ -z \"\$DISPLAY\" -a \"X\$TERM_PROGRAM\" = \"XApple_Terminal\" \]; then'
fsl-5.0.8/doc/fsl/fsl_installer.sh:217: elif [ `is_csh ${display_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-218- remove='if ( \$?TERM_PROGRAM ) then'
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-222- fi
fsl-5.0.8/doc/fsl/fsl_installer.sh:223: if [ -n "`grep \"${remove}\" ${display_profile}`" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-224- # Remove the section
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-231- diff ${display_profile}.bak ${display_profile} | sed -e '1d' -e 's/^> //' | sed -e :a -e '/^\n*$/{$d;N;};/\n$/ba' > ${test_file}.bak
fsl-5.0.8/doc/fsl/fsl_installer.sh:232: if [ -n "`diff \"${test_file}\" \"${test_file}.bak\"`" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-233- echo "Remove failed (maybe you added DISPLAY settings yourself) - please update your ${display_profile} by hand"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-249- if [ -f ${apple_profile} ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:250: if [ -n "`grep 'DISPLAY' ${apple_profile}`" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-251- echo "You are running Mac OS X 10.5 and have DISPLAY configured in your ${apple_profile} file."
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-258- if [ -f ${apple_profile} ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:259: if [ `grep DISPLAY ${apple_profile} | wc -l` -gt 0 ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-260- echo "DISPLAY is already being configured in your '${apple_profile}' - not changing"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-264-
fsl-5.0.8/doc/fsl/fsl_installer.sh:265: if [ `is_csh ${apple_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-266- cat <<CSH_TERM >>${apple_profile}
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-268- if ( "X\$TERM_PROGRAM" == "XApple_Terminal" ) then; if ( ! \$?DISPLAY ) then
fsl-5.0.8/doc/fsl/fsl_installer.sh:269: set X11_FOLDER=/tmp/.X11-unix; set currentUser=\`id -u\`; set userX11folder=\`find \$X11_FOLDER -name 'X*' -user \$currentUser -print | tail -n 1\`
fsl-5.0.8/doc/fsl/fsl_installer.sh-270- if ( "X\$userX11folder" != "X" ) then
fsl-5.0.8/doc/fsl/fsl_installer.sh:271: set displaynumber=\`basename \${userX11folder} | grep -o '[[:digit:]]\+'\`
fsl-5.0.8/doc/fsl/fsl_installer.sh-272- if ( "X\$displaynumber" != "X" ) then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-282-CSH_TERM
fsl-5.0.8/doc/fsl/fsl_installer.sh:283: elif [ `is_sh ${apple_profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-284- cat <<SH_TERM >>${apple_profile}
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-287- currentUser=\`id -u\`
fsl-5.0.8/doc/fsl/fsl_installer.sh:288: userX11folder=\`find \$X11_FOLDER -name 'X*' -user \$currentUser -print 2>&1 | tail -n 1\`
fsl-5.0.8/doc/fsl/fsl_installer.sh-289- if [ -n "\$userX11folder" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:290: displaynumber=\`basename \${userX11folder} | grep -o '[[:digit:]]\+'\`
fsl-5.0.8/doc/fsl/fsl_installer.sh-291- if [ -n "\$displaynumber" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-314- if [ -e ${m_startup} ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:315: if [ -z "`grep FSLDIR ${m_startup}`" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-316- echo "Configuring Matlab..."
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-333- if [ "X${install_location}" = "X-NONE-" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:334: install_location=`get_fsldir ${default_location} 1 "Where is FSL installed? [${default_location}]"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-335- fi
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-370- my_home=${HOME}
fsl-5.0.8/doc/fsl/fsl_installer.sh:371: my_shell=`basename ${SHELL}`
fsl-5.0.8/doc/fsl/fsl_installer.sh-372- env_modified="0"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-409- if [ -f ${my_home}/${profile} ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:410: if [ `is_csh ${my_home}/${profile}` ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-411- search_string="setenv FSLDIR ${install_location}/fsl\$"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-414- fi
fsl-5.0.8/doc/fsl/fsl_installer.sh:415: fsldir_defs=`cat ${my_home}/${profile} | grep "FSLDIR" | wc -l`
fsl-5.0.8/doc/fsl/fsl_installer.sh-416- if [ $fsldir_defs -gt 0 ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-417- output="${profile} already contains a FSLDIR definition"
fsl-5.0.8/doc/fsl/fsl_installer.sh:418: if [ -n "`cat ${my_home}/${profile} | grep \"${search_string}\"`" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-419- echo "${output} which is correctly configured, not changing."
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-546- else
fsl-5.0.8/doc/fsl/fsl_installer.sh:547: test_tarball=`file -b "${tarball}" | grep '\(gzip\)\|\(tar\)'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-548- if [ -z "${test_tarball}" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-554- if [ $? = 0 ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:555: message=`check_digest "${tarball}" "${install_from}" "${digest_dir}"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-556- status=$?
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-636- fi
fsl-5.0.8/doc/fsl/fsl_installer.sh:637: my_LD_v=`(cd ${my_LD}; ls ld-*.so| sed -n 's/ld-\([0-9]*\)\.\([0-9]*\)\(.[0-9]*\)*.so/\1\2/p')`
fsl-5.0.8/doc/fsl/fsl_installer.sh-638-
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-653- esac
fsl-5.0.8/doc/fsl/fsl_installer.sh:654: prev_centos=`expr $centos_v - 1`
fsl-5.0.8/doc/fsl/fsl_installer.sh:655: next_centos=`expr $centos_v + 1`
fsl-5.0.8/doc/fsl/fsl_installer.sh-656-
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-709- fi
fsl-5.0.8/doc/fsl/fsl_installer.sh:710: choice=`to_lower ${choice}`
fsl-5.0.8/doc/fsl/fsl_installer.sh-711- echo $choice
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-749-
fsl-5.0.8/doc/fsl/fsl_installer.sh:750: my_patches=`echo $tarb | sed -n 's/fsl-.*-patch-[0-9.]*_from_\([0-9x.]*\).tar\(.gz\)/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:751: my_to=`echo $tarb | sed -n 's/fsl-.*-patch-\([0-9.]*\)_from_[0-9x.]*.tar\(.gz\)/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:752: my_major=`echo $my_patches | sed -n 's/\([0-9]*\).[0-9]*.[0-9x]*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:753: my_minor=`echo $my_patches | sed -n 's/[0-9]*.\([0-9]*\).[0-9x]*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:754: my_patch=`echo $my_patches | sed -n 's/[0-9]*.[0-9]*.\([0-9x]*\)/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-755-
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-760-
fsl-5.0.8/doc/fsl/fsl_installer.sh:761: my_fslversion=`cat ${installed_dir}/fsl/etc/fslversion`
fsl-5.0.8/doc/fsl/fsl_installer.sh:762: my_fslmaj=`echo $my_fslversion | sed -n 's/\([0-9]*\).[0-9]*.[0-9]*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:763: my_fslmin=`echo $my_fslversion | sed -n 's/[0-9]*.\([0-9]*\).[0-9]*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:764: my_fslpatch=`echo $my_fslversion | sed -n 's/[0-9]*.[0-9]*.\([0-9]*\)/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-765-
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-797-
fsl-5.0.8/doc/fsl/fsl_installer.sh:798: tgz_platform=`echo $tarball | grep -o 'centos\|macosx'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-799-
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-802- if [ "X$tgz_platform" = "Xcentos" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:803: my_centosrelease=`echo $tarball | sed -n 's/fsl-.*centos\([0-9]*\)_[0-9]*\(-patch.*\)*.tar\(.gz\)*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh:804: my_bitdepth=`echo $tarball | sed -n 's/fsl-.*centos[0-9]*_\([0-9]*\)\(-patch.*\)*.tar\(.gz\)*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-805- if [ "X$my_centosrelease" != "X" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:806: message=`check_glibc ${my_centosrelease} ${my_bitdepth}`
fsl-5.0.8/doc/fsl/fsl_installer.sh-807- status=$?
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-860- # First check the tarball is the right version
fsl-5.0.8/doc/fsl/fsl_installer.sh:861: my_bitdepth=`echo $tarball | sed -n 's/fsl-.*_\([0-9]*\)\(-patch.*\)*.tar\(.gz\)*/\1/p'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-862- if [ "X$my_bitdepth" != "X" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh-863- # This is not a bit agnostic install, check the tarball is the correct version
fsl-5.0.8/doc/fsl/fsl_installer.sh:864: message=`check_platform $my_bitdepth`
fsl-5.0.8/doc/fsl/fsl_installer.sh-865- status=$?
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-918- echo "Checking OS release ..."
fsl-5.0.8/doc/fsl/fsl_installer.sh:919: message=`check_tarball_os $tarball`
fsl-5.0.8/doc/fsl/fsl_installer.sh-920- ok_or_exit $? "$message"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-922- echo "Checking CPU type..."
fsl-5.0.8/doc/fsl/fsl_installer.sh:923: message=`check_tarball_bits $tarball`
fsl-5.0.8/doc/fsl/fsl_installer.sh-924- ok_or_exit $? "$message"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-927- echo "Checking FSL release..."
fsl-5.0.8/doc/fsl/fsl_installer.sh:928: message=`check_patch_version $tarball "$install_location"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-929- ok_or_exit $? "$message"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-932- echo "Checking install file...(this may take several minutes)"
fsl-5.0.8/doc/fsl/fsl_installer.sh:933: message=`verify_tarball ${tarball} "${install_from}" ${fsl_server} ${fsl_dir} "${temp_dir}" ${no_md5}`
fsl-5.0.8/doc/fsl/fsl_installer.sh-934- ok_or_exit $? "$message"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-936- echo "Installing FSL from ${install_from}/${tarball} into ${install_location}..."
fsl-5.0.8/doc/fsl/fsl_installer.sh:937: message=`install_tarball ${tarball} "${install_from}" "${install_location}" ${need_sudo}`
fsl-5.0.8/doc/fsl/fsl_installer.sh-938- ok_or_exit $? "$message"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-945- fi
fsl-5.0.8/doc/fsl/fsl_installer.sh:946: choice=`to_lower $choice`;
fsl-5.0.8/doc/fsl/fsl_installer.sh-947- if [ "X$choice" = "Xyes" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-983-to_lower () {
fsl-5.0.8/doc/fsl/fsl_installer.sh:984: echo `echo $1 | tr 'A-Z' 'a-z'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-985-}
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1035- read -p "'${choice}' doesn't exist, would you like me to create it? [yes] " >&2 yesno
fsl-5.0.8/doc/fsl/fsl_installer.sh:1036: yesno=`to_lower ${yesno}`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1037- if [ -z "${yesno}" -o "X${yesno}" = "Xyes" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1142- echo "Looking for FSL tarball in the current directory..."
fsl-5.0.8/doc/fsl/fsl_installer.sh:1143: tarballs=`ls "${here}" | grep '^fsl-.*.tar\(.gz\)*$' | wc -l`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1144-
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1151- else
fsl-5.0.8/doc/fsl/fsl_installer.sh:1152: fsl_tarball=`ls "${here}" | grep '^fsl-.*.tar\(.gz\)*$'`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1153- fsl_tarball="$here/$fsl_tarball"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1168-
fsl-5.0.8/doc/fsl/fsl_installer.sh:1169: install_from=`dirname "${fsl_tarball}"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1170- if [ -z "${install_from}" -o "X$install_from" = "X." ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1172- else
fsl-5.0.8/doc/fsl/fsl_installer.sh:1173: fsl_tarball=`basename "${fsl_tarball}"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1174- fi
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1176- # Check if it is a patch file
fsl-5.0.8/doc/fsl/fsl_installer.sh:1177: test_patchfile=`echo "${fsl_tarball}" | grep patch`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1178- if [ -n "${test_patchfile}" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1184- if [ "X${install_location}" = "X-NONE-" ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:1185: install_location=`get_fsldir "${default_location}" 0 "Where would you like to install FSL to? [${default_location}] "`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1186- fi
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1190- read -p "'${install_location}' doesn't exist, would you like me to create it? [yes] " >&2 choice
fsl-5.0.8/doc/fsl/fsl_installer.sh:1191: choice=`to_lower $choice`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1192- if [ -z "${choice}" -o "X${choice}" = "Xyes" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1214- # Check it is writeable, and if not request Sudo
fsl-5.0.8/doc/fsl/fsl_installer.sh:1215: writeable=`touch "${install_location}/.fsl-test" 2>&1 | grep "Permission denied"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1216- echo "$writeable"
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1239- read -p "'${install_location}/fsl' exists - would you like to remove it? [yes] " >&2 choice
fsl-5.0.8/doc/fsl/fsl_installer.sh:1240: choice=`to_lower $choice`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1241- if [ -z "${choice}" -o "X${choice}" = "Xyes" ]; then
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1268- if [ "X${install_location}" = 'X-NONE-' ]; then
fsl-5.0.8/doc/fsl/fsl_installer.sh:1269: install_location=`get_fsldir ${default_location} 1 "Where is FSL installed? [${default_location}]"`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1270- fi
##############################################
fsl-5.0.8/doc/fsl/fsl_installer.sh-1277- read -p "Would you like to configure FSL system wide? (Not recommended if ${install_location} is on an NFS share) [no] " >&2 choice
fsl-5.0.8/doc/fsl/fsl_installer.sh:1278: choice=`to_lower $choice`
fsl-5.0.8/doc/fsl/fsl_installer.sh-1279- if [ "X${choice}" = "Xyes" ]; then
##############################################
fsl-5.0.8/doc/fsl/macosx.html-199- currentUser=`id -u`
fsl-5.0.8/doc/fsl/macosx.html:200: userX11folder=`find $X11_FOLDER -name 'X*' -user $currentUser -print 2>&1 | tail -n 1`
fsl-5.0.8/doc/fsl/macosx.html-201- if [ -n "$userX11folder" ]; then
fsl-5.0.8/doc/fsl/macosx.html:202: displaynumber=`basename ${userX11folder} | grep -o '[[:digit:]]\+'`
fsl-5.0.8/doc/fsl/macosx.html-203- if [ -n "$displaynumber" ]; then
##############################################
fsl-5.0.8/doc/fsl/macosx.html-233- if ( "X$TERM_PROGRAM" == "XApple_Terminal" ) then; if ( ! $?DISPLAY ) then
fsl-5.0.8/doc/fsl/macosx.html:234: set X11_FOLDER=/tmp/.X11-unix; set currentUser=`id -u`; set userX11folder=`find $X11_FOLDER -name 'X*' -user $currentUser -print | tail -n 1`
fsl-5.0.8/doc/fsl/macosx.html-235- if ( "X$userX11folder" != "X" ) then
fsl-5.0.8/doc/fsl/macosx.html:236: set displaynumber=`basename ${userX11folder} | grep -o '[[:digit:]]\+'`
fsl-5.0.8/doc/fsl/macosx.html-237- if ( "X$displaynumber" != "X" ) then
##############################################
fsl-5.0.8/src/bet2/bet-114-get_dims() {
fsl-5.0.8/src/bet2/bet:115: xdim=`${FSLDIR}/bin/fslval $1 dim1 | sed 's/-//g'`
fsl-5.0.8/src/bet2/bet:116: ydim=`${FSLDIR}/bin/fslval $1 dim2 | sed 's/-//g'`
fsl-5.0.8/src/bet2/bet:117: zdim=`${FSLDIR}/bin/fslval $1 dim3 | sed 's/-//g'`
fsl-5.0.8/src/bet2/bet:118: xpixdim=`${FSLDIR}/bin/fslval $1 pixdim1 | sed 's/-//g'`
fsl-5.0.8/src/bet2/bet:119: ypixdim=`${FSLDIR}/bin/fslval $1 pixdim2 | sed 's/-//g'`
fsl-5.0.8/src/bet2/bet:120: zpixdim=`${FSLDIR}/bin/fslval $1 pixdim3 | sed 's/-//g'`
fsl-5.0.8/src/bet2/bet-121- #echo $xdim $ydim $zdim $xpixdim $ypixdim $zpixdim
##############################################
fsl-5.0.8/src/bet2/bet-127-# find_centre_in_mm() {
fsl-5.0.8/src/bet2/bet:128:# centre=`${FSLDIR}/bin/fslstats $1 -l 0.001 -C`
fsl-5.0.8/src/bet2/bet:129:# x=`echo $centre $xpixdim | awk '{print "10 k " $1 " " $4 " * p"}' | dc -`
fsl-5.0.8/src/bet2/bet:130:# y=`echo $centre $ypixdim | awk '{print "10 k " $2 " " $4 " * p"}' | dc -`
fsl-5.0.8/src/bet2/bet:131:# z=`echo $centre $zpixdim | awk '{print "10 k " $3 " " $4 " * p"}' | dc -`
fsl-5.0.8/src/bet2/bet-132-# #echo $x $y $z
##############################################
fsl-5.0.8/src/bet2/bet-138-find_centre_in_voxels() {
fsl-5.0.8/src/bet2/bet:139: centre=`${FSLDIR}/bin/fslstats $1 -l 0.001 -C`
fsl-5.0.8/src/bet2/bet:140: x=`echo $centre | awk '{print $1}'`
fsl-5.0.8/src/bet2/bet:141: y=`echo $centre | awk '{print $2}'`
fsl-5.0.8/src/bet2/bet:142: z=`echo $centre | awk '{print $3}'`
fsl-5.0.8/src/bet2/bet-143- #echo $x $y $z
##############################################
fsl-5.0.8/src/bet2/bet-150-[ "$2" = "" ] && Usage
fsl-5.0.8/src/bet2/bet:151:IN=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/bet2/bet:152:OUT=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/bet2/bet-153-shift 2
fsl-5.0.8/src/bet2/bet:154:if [ `${FSLDIR}/bin/imtest $IN` = 0 ] ; then
fsl-5.0.8/src/bet2/bet-155- echo ""
##############################################
fsl-5.0.8/src/bet2/bet-239-
fsl-5.0.8/src/bet2/bet:240:bet2opts=`echo $bet2opts | sed 's/-n//g'`
fsl-5.0.8/src/bet2/bet-241-get_dims $IN
##############################################
fsl-5.0.8/src/bet2/bet-252- find_centre_in_voxels $OUT
fsl-5.0.8/src/bet2/bet:253: diffsq=`echo "0 k $ox $x - 2 ^ $oy $y - 2 ^ + $oz $z - 2 ^ + 1 / p" | dc -`
fsl-5.0.8/src/bet2/bet-254- #echo $diffsq
##############################################
fsl-5.0.8/src/bet2/bet-258- fi
fsl-5.0.8/src/bet2/bet:259: i=`echo "$i 1 + p" | dc -`
fsl-5.0.8/src/bet2/bet-260-done
##############################################
fsl-5.0.8/src/bet2/bet-281-#### find upper threshold used to delete eyes
fsl-5.0.8/src/bet2/bet:282:Mean=`${FSLDIR}/bin/fslstats ${OUT}_tmp_prebrain -M`
fsl-5.0.8/src/bet2/bet:283:SD=`${FSLDIR}/bin/fslstats ${OUT}_tmp_prebrain -S`
fsl-5.0.8/src/bet2/bet:284:thr=`echo "10 k 3.5 $SD * $Mean + p" | dc -`
fsl-5.0.8/src/bet2/bet-285-
##############################################
fsl-5.0.8/src/bet2/bet-300-
fsl-5.0.8/src/bet2/bet:301:npad=`echo "$MINZFOV $zpixdim / $zdim - 2 / 1 + p" | dc -`
fsl-5.0.8/src/bet2/bet-302-
##############################################
fsl-5.0.8/src/bet2/bet-309-${FSLDIR}/bin/fslroi $IN ${OUT}_tmp_bottom 0 $xdim 0 $ydim 0 1
fsl-5.0.8/src/bet2/bet:310:${FSLDIR}/bin/fslroi $IN ${OUT}_tmp_top 0 $xdim 0 $ydim `echo "$zdim 1 - p" | dc -` 1
fsl-5.0.8/src/bet2/bet-311-
##############################################
fsl-5.0.8/src/bet2/bet-315- toplist="$toplist ${OUT}_tmp_top"
fsl-5.0.8/src/bet2/bet:316: n=`echo "$n 1 + p" | dc -`
fsl-5.0.8/src/bet2/bet-317-done
##############################################
fsl-5.0.8/src/bet2/bet-322-
fsl-5.0.8/src/bet2/bet:323:for f in `imglob ${OUT}*` ; do
fsl-5.0.8/src/bet2/bet-324- ${FSLDIR}/bin/fslroi $f $f 0 $xdim 0 $ydim $npad $zdim
##############################################
fsl-5.0.8/src/bet2/bet-381- ${FSLDIR}/bin/bet2 ${OUT}_tmp_unbiased_forskull_reduced ${OUT}_tmp_unbiased_forskull $bet2opts
fsl-5.0.8/src/bet2/bet:382: bet2opts=`echo $bet2opts | sed 's/-s//g'`
fsl-5.0.8/src/bet2/bet-383- ${FSLDIR}/bin/immv ${OUT}_tmp_unbiased_forskull_skull ${OUT}_skull
##############################################
fsl-5.0.8/src/bet2/old_betall-79-[ "$2" = "" ] && Usage
fsl-5.0.8/src/bet2/old_betall:80:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/bet2/old_betall:81:[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
fsl-5.0.8/src/bet2/old_betall:82:A1=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/bet2/old_betall:83:A2=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/bet2/old_betall-84-
##############################################
fsl-5.0.8/src/randomise/setup_masks-67-Usage() {
fsl-5.0.8/src/randomise/setup_masks:68: echo "`basename $0` <input matrix> <input contrast> <output basename> <mask1> <mask2> ..."
fsl-5.0.8/src/randomise/setup_masks-69- echo " "
##############################################
fsl-5.0.8/src/randomise/setup_masks-79-if [ $# -lt 4 ] ; then Usage; fi
fsl-5.0.8/src/randomise/setup_masks:80:numsubj=`echo $# - 3 | bc`
fsl-5.0.8/src/randomise/setup_masks-81-
##############################################
fsl-5.0.8/src/randomise/setup_masks-95-# sanity check on size of matrix
fsl-5.0.8/src/randomise/setup_masks:96:maxrow=`cat ${out}.mat.txt | wc -l`;
fsl-5.0.8/src/randomise/setup_masks-97-if [ $maxrow != $numsubj ] ; then
##############################################
fsl-5.0.8/src/randomise/setup_masks-100-fi
fsl-5.0.8/src/randomise/setup_masks:101:maxcol=`cat ${out}.mat.txt | wc -w`;
fsl-5.0.8/src/randomise/setup_masks:102:maxcol=`echo $maxcol / $maxrow | bc`;
fsl-5.0.8/src/randomise/setup_masks-103-echo "MATRIX SIZE IS $maxrow $maxcol"
##############################################
fsl-5.0.8/src/randomise/setup_masks-113-while [ $subjnum -lt $numsubj ] ; do
fsl-5.0.8/src/randomise/setup_masks:114: znum=`echo $subjnum + $maxcol + 1 | bc`
fsl-5.0.8/src/randomise/setup_masks-115- vxlopts="${vxlopts},${znum}";
fsl-5.0.8/src/randomise/setup_masks:116: znum=`$FSLDIR/bin/zeropad $znum 4`;
fsl-5.0.8/src/randomise/setup_masks-117- $FSLDIR/bin/fslmaths $out -roi 0 -1 0 -1 0 -1 $subjnum 1 ${out}_${znum}
fsl-5.0.8/src/randomise/setup_masks-118- vxfopts="${vxfopts},${out}_${znum}";
fsl-5.0.8/src/randomise/setup_masks:119: subjnum=`echo $subjnum + 1 | bc`;
fsl-5.0.8/src/randomise/setup_masks-120-done
##############################################
fsl-5.0.8/src/randomise/setup_masks-136- zerocon="${zerocon} 0"
fsl-5.0.8/src/randomise/setup_masks:137: col=`echo $col + 1 | bc`;
fsl-5.0.8/src/randomise/setup_masks-138- done ;
fsl-5.0.8/src/randomise/setup_masks-139- echo "$cs" >> ${out}.mat.ext ;
fsl-5.0.8/src/randomise/setup_masks:140: row=`echo $row + 1 | bc` ;
fsl-5.0.8/src/randomise/setup_masks-141-done
##############################################
fsl-5.0.8/src/randomise/setup_masks-143-ncon=1;
fsl-5.0.8/src/randomise/setup_masks:144:totcon=`cat ${out}.con.txt | wc -l`;
fsl-5.0.8/src/randomise/setup_masks-145-while [ $ncon -le $totcon ] ; do
fsl-5.0.8/src/randomise/setup_masks-146- echo $zerocon >> ${out}.con.ext
fsl-5.0.8/src/randomise/setup_masks:147: ncon=`echo $ncon + 1 | bc`;
fsl-5.0.8/src/randomise/setup_masks-148-done
##############################################
fsl-5.0.8/src/randomise/design_ttest2-78-NB=$3
fsl-5.0.8/src/randomise/design_ttest2:79:NAandB=`echo "$NA $NB + p" | dc -`
fsl-5.0.8/src/randomise/design_ttest2-80-
##############################################
fsl-5.0.8/src/randomise/design_ttest2-86- echo "1 0" >> ${OUT}.mat
fsl-5.0.8/src/randomise/design_ttest2:87: NA=`echo "$NA 1 - p" | dc -`
fsl-5.0.8/src/randomise/design_ttest2-88-done
##############################################
fsl-5.0.8/src/randomise/design_ttest2-90- echo "0 1" >> ${OUT}.mat
fsl-5.0.8/src/randomise/design_ttest2:91: NB=`echo "$NB 1 - p" | dc -`
fsl-5.0.8/src/randomise/design_ttest2-92-done
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-76-
fsl-5.0.8/src/randomise/randomise_parallel:77:RANDOMISE_OUTPUT=`$FSLDIR/bin/randomise $@ -Q`
fsl-5.0.8/src/randomise/randomise_parallel-78-if [ $? != 0 ] ; then
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-82-
fsl-5.0.8/src/randomise/randomise_parallel:83:PERMS=`echo $RANDOMISE_OUTPUT | awk '{print $1}'`
fsl-5.0.8/src/randomise/randomise_parallel:84:CONTRASTS=`echo $RANDOMISE_OUTPUT | awk '{print $2}'`
fsl-5.0.8/src/randomise/randomise_parallel:85:ROOTNAME=`echo $RANDOMISE_OUTPUT | awk '{print $3}'`
fsl-5.0.8/src/randomise/randomise_parallel:86:BASENAME=`basename $ROOTNAME`
fsl-5.0.8/src/randomise/randomise_parallel:87:DIRNAME=`dirname $ROOTNAME`
fsl-5.0.8/src/randomise/randomise_parallel-88-
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-90-
fsl-5.0.8/src/randomise/randomise_parallel:91:PERMS_PER_SLOT=`echo $RANDOMISE_OUTPUT | awk '{print $4}'`
fsl-5.0.8/src/randomise/randomise_parallel-92-if [ x${REQUESTED_TIME} = 'x' ] ; then
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-95-
fsl-5.0.8/src/randomise/randomise_parallel:96:SLOTS_PER_CONTRAST=`expr $PERMS / $PERMS_PER_SLOT`
fsl-5.0.8/src/randomise/randomise_parallel-97-
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-101-
fsl-5.0.8/src/randomise/randomise_parallel:102:PERMS_PER_CONTRAST=`expr $PERMS_PER_SLOT \* $SLOTS_PER_CONTRAST`
fsl-5.0.8/src/randomise/randomise_parallel-103-
fsl-5.0.8/src/randomise/randomise_parallel:104:REQUESTED_SLOTS=`expr $CONTRASTS \* $SLOTS_PER_CONTRAST`
fsl-5.0.8/src/randomise/randomise_parallel-105-
fsl-5.0.8/src/randomise/randomise_parallel:106:CORRECTED_PERMS=`expr $PERMS_PER_CONTRAST - $SLOTS_PER_CONTRAST`
fsl-5.0.8/src/randomise/randomise_parallel:107:CORRECTED_PERMS=`expr $CORRECTED_PERMS + 1`
fsl-5.0.8/src/randomise/randomise_parallel-108-
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-117-while [ $CURRENT_SEED -le $SLOTS_PER_CONTRAST ] ; do
fsl-5.0.8/src/randomise/randomise_parallel:118: SLEEPTIME=`expr 1 \* $CURRENT_SEED`
fsl-5.0.8/src/randomise/randomise_parallel-119- CURRENT_CONTRAST=1
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-121- echo "FSLOUTPUTTYPE=NIFTI_GZ; sleep $SLEEPTIME ; ${FSLDIR}/bin/randomise $@ -n $PERMS_PER_SLOT -o ${ROOTNAME}_SEED${CURRENT_SEED} --seed=$CURRENT_SEED --skipTo=$CURRENT_CONTRAST" >> ${DIRNAME}/${BASENAME}.generate
fsl-5.0.8/src/randomise/randomise_parallel:122: CURRENT_CONTRAST=`expr $CURRENT_CONTRAST + 1`
fsl-5.0.8/src/randomise/randomise_parallel-123- done
fsl-5.0.8/src/randomise/randomise_parallel-124- echo done $CURRENT_SEED
fsl-5.0.8/src/randomise/randomise_parallel:125: CURRENT_SEED=`expr $CURRENT_SEED + 1`
fsl-5.0.8/src/randomise/randomise_parallel-126-done
fsl-5.0.8/src/randomise/randomise_parallel-127-chmod a+x ${DIRNAME}/${BASENAME}.generate
fsl-5.0.8/src/randomise/randomise_parallel:128:GENERATE_ID=`$FSLDIR/bin/fsl_sub -T ${REQUESTED_TIME} -N ${BASENAME}.generate -l ${DIRNAME}/${BASENAME}_logs/ -t ${DIRNAME}/${BASENAME}.generate`
fsl-5.0.8/src/randomise/randomise_parallel-129-
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-138- while [ \$ACTIVESEED -le $SLOTS_PER_CONTRAST ] ; do
fsl-5.0.8/src/randomise/randomise_parallel:139: ADDCOMMAND=\`echo \$ADDCOMMAND -add \${FIRSTSEED/_SEED1_/_SEED\${ACTIVESEED}_}\`
fsl-5.0.8/src/randomise/randomise_parallel:140: ACTIVESEED=\`expr \$ACTIVESEED + 1\`
fsl-5.0.8/src/randomise/randomise_parallel-141- done
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-157- fi
fsl-5.0.8/src/randomise/randomise_parallel:158: ACTIVESEED=\`expr \$ACTIVESEED + 1\`
fsl-5.0.8/src/randomise/randomise_parallel-159- done
##############################################
fsl-5.0.8/src/randomise/randomise_parallel-181-
fsl-5.0.8/src/randomise/randomise_parallel:182: ACTIVESEED=\`expr \$ACTIVESEED + 1\`
fsl-5.0.8/src/randomise/randomise_parallel-183-done
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-113-
fsl-5.0.8/src/flirt/standard_space_roi:114:in=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/flirt/standard_space_roi:115:if [ `${FSLDIR}/bin/imtest $in` = 0 ] ; then
fsl-5.0.8/src/flirt/standard_space_roi-116- echo "Input image $in not valid"
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-120-
fsl-5.0.8/src/flirt/standard_space_roi:121:out=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/flirt/standard_space_roi-122-shift
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-147- shift 2
fsl-5.0.8/src/flirt/standard_space_roi:148: if [ `${FSLDIR}/bin/imtest $standard` = 0 ] ; then
fsl-5.0.8/src/flirt/standard_space_roi-149- echo "standard space reference image not valid"
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-155- shift 2
fsl-5.0.8/src/flirt/standard_space_roi:156: if [ `${FSLDIR}/bin/imtest $inapply` = 0 ] ; then
fsl-5.0.8/src/flirt/standard_space_roi-157- echo "Input image $inapply not valid"
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-168- shift 2
fsl-5.0.8/src/flirt/standard_space_roi:169: if [ `${FSLDIR}/bin/imtest $roimask` = 0 ] ; then
fsl-5.0.8/src/flirt/standard_space_roi-170- echo "Image $roimask not valid"
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-184- shift 2
fsl-5.0.8/src/flirt/standard_space_roi:185: if [ `${FSLDIR}/bin/imtest $maskmask` = 0 ] ; then
fsl-5.0.8/src/flirt/standard_space_roi-186- echo "Image $maskmask not valid"
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-213-
fsl-5.0.8/src/flirt/standard_space_roi:214:X=`${FSLDIR}/bin/fslval $standard dim1` ; X=`echo "$X 2 - p" | dc -`
fsl-5.0.8/src/flirt/standard_space_roi:215:Y=`${FSLDIR}/bin/fslval $standard dim2` ; Y=`echo "$Y 2 - p" | dc -`
fsl-5.0.8/src/flirt/standard_space_roi:216:Z=`${FSLDIR}/bin/fslval $standard dim3` ; Z=`echo "$Z 2 - p" | dc -`
fsl-5.0.8/src/flirt/standard_space_roi-217-
##############################################
fsl-5.0.8/src/flirt/standard_space_roi-238- ${FSLDIR}/bin/flirt -ref $in -in ${out}_tmp_standard_roi -o ${out}_tmp_standard_roi_to_in -applyxfm -init ${out}_tmp_to_std_inv.mat
fsl-5.0.8/src/flirt/standard_space_roi:239: ${FSLDIR}/bin/fslroi $inapply $out `${FSLDIR}/bin/fslstats ${out}_tmp_standard_roi_to_in -w`
fsl-5.0.8/src/flirt/standard_space_roi-240-else
##############################################
fsl-5.0.8/src/flirt/flirt_average-89-
fsl-5.0.8/src/flirt/flirt_average:90:reference=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/flirt/flirt_average-91-
##############################################
fsl-5.0.8/src/flirt/flirt_average-93-while [ $i -le $N ] ; do
fsl-5.0.8/src/flirt/flirt_average:94: imagelist="$imagelist `${FSLDIR}/bin/remove_ext $1`"
fsl-5.0.8/src/flirt/flirt_average-95- shift
fsl-5.0.8/src/flirt/flirt_average:96: i=`echo "$i 1 + p" | dc -`
fsl-5.0.8/src/flirt/flirt_average-97-done
##############################################
fsl-5.0.8/src/flirt/flirt_average-104- if [ $1 = -FAref ] ; then
fsl-5.0.8/src/flirt/flirt_average:105: reference=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/flirt/flirt_average-106- shift 2
##############################################
fsl-5.0.8/src/flirt/extracttxt-69-fi
fsl-5.0.8/src/flirt/extracttxt:70:num=`grep -n $1 $2 | head -n 1 | cut -d':' -f1 ` ; export num
fsl-5.0.8/src/flirt/extracttxt-71-if [ X${num}X != XX ] ; then
##############################################
fsl-5.0.8/src/flirt/extracttxt-73- if [ $4 -ge 0 ] ; then
fsl-5.0.8/src/flirt/extracttxt:74: num1=` echo "$num $4 + p" | dc -` ; export num1
fsl-5.0.8/src/flirt/extracttxt-75- else
fsl-5.0.8/src/flirt/extracttxt:76: num1=` echo "0 0 $4 - $num + p" | dc -` ; export num1
fsl-5.0.8/src/flirt/extracttxt-77- fi
##############################################
fsl-5.0.8/src/flirt/extracttxt-81- if [ $# -ge 3 ]; then
fsl-5.0.8/src/flirt/extracttxt:82: num2=` echo "$num1 $3 + 1 - p" | dc -` ; export num2
fsl-5.0.8/src/flirt/extracttxt-83- if [ $num2 -lt $num1 ]; then
##############################################
fsl-5.0.8/src/flirt/epi_reg-67- echo ""
fsl-5.0.8/src/flirt/epi_reg:68: echo "Usage: `basename $0` [options] --epi=<EPI image> --t1=<wholehead T1 image> --t1brain=<brain extracted T1 image> --out=<output name>"
fsl-5.0.8/src/flirt/epi_reg-69- echo " "
##############################################
fsl-5.0.8/src/flirt/epi_reg-82- echo " "
fsl-5.0.8/src/flirt/epi_reg:83: echo "e.g.: `basename $0` --epi=example_func --t1=struct --t1brain=struct_brain --out=epi2struct --fmap=fmap_rads --fmapmag=fmap_mag --fmapmagbrain=fmap_mag_brain --echospacing=0.0005 --pedir=-y"
fsl-5.0.8/src/flirt/epi_reg-84- echo " "
##############################################
fsl-5.0.8/src/flirt/epi_reg-92-get_opt1() {
fsl-5.0.8/src/flirt/epi_reg:93: arg=`echo $1 | sed 's/=.*//'`
fsl-5.0.8/src/flirt/epi_reg-94- echo $arg
##############################################
fsl-5.0.8/src/flirt/epi_reg-98-get_arg1() {
fsl-5.0.8/src/flirt/epi_reg:99: if [ X`echo $1 | grep '='` = X ] ; then
fsl-5.0.8/src/flirt/epi_reg-100- echo "Option $1 requires an argument" 1>&2
##############################################
fsl-5.0.8/src/flirt/epi_reg-102- else
fsl-5.0.8/src/flirt/epi_reg:103: arg=`echo $1 | sed 's/.*=//'`
fsl-5.0.8/src/flirt/epi_reg-104- if [ X$arg = X ] ; then
##############################################
fsl-5.0.8/src/flirt/epi_reg-112-get_imarg1() {
fsl-5.0.8/src/flirt/epi_reg:113: arg=`get_arg1 $1`;
fsl-5.0.8/src/flirt/epi_reg:114: arg=`$FSLDIR/bin/remove_ext $arg`;
fsl-5.0.8/src/flirt/epi_reg-115- echo $arg
##############################################
fsl-5.0.8/src/flirt/epi_reg-149-while [ $# -ge 1 ] ; do
fsl-5.0.8/src/flirt/epi_reg:150: iarg=`get_opt1 $1`;
fsl-5.0.8/src/flirt/epi_reg-151- case "$iarg"
##############################################
fsl-5.0.8/src/flirt/epi_reg-153- --epi)
fsl-5.0.8/src/flirt/epi_reg:154: vepi=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-155- shift;;
fsl-5.0.8/src/flirt/epi_reg-156- --t1)
fsl-5.0.8/src/flirt/epi_reg:157: vrefhead=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-158- shift;;
fsl-5.0.8/src/flirt/epi_reg-159- --t1brain)
fsl-5.0.8/src/flirt/epi_reg:160: vrefbrain=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-161- shift;;
fsl-5.0.8/src/flirt/epi_reg-162- --fmap)
fsl-5.0.8/src/flirt/epi_reg:163: fmaprads=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-164- use_fmap=yes;
##############################################
fsl-5.0.8/src/flirt/epi_reg-166- --fmapmag)
fsl-5.0.8/src/flirt/epi_reg:167: fmapmaghead=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-168- shift;;
fsl-5.0.8/src/flirt/epi_reg-169- --fmapmagbrain)
fsl-5.0.8/src/flirt/epi_reg:170: fmapmagbrain=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-171- shift;;
fsl-5.0.8/src/flirt/epi_reg-172- --wmseg)
fsl-5.0.8/src/flirt/epi_reg:173: wmseg=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-174- shift;;
fsl-5.0.8/src/flirt/epi_reg-175- --out)
fsl-5.0.8/src/flirt/epi_reg:176: vout=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-177- shift;;
fsl-5.0.8/src/flirt/epi_reg-178- --echospacing)
fsl-5.0.8/src/flirt/epi_reg:179: dwell=`get_arg1 $1`;
fsl-5.0.8/src/flirt/epi_reg:180: if [ `echo "if ( $dwell > 0.2 ) {1}; if ( $dwell <= 0.2 ) {0}" | bc -l` = 1 ] ; then
fsl-5.0.8/src/flirt/epi_reg:181: msdwell=`echo "scale=6; $dwell / 1000.0" | bc -l`;
fsl-5.0.8/src/flirt/epi_reg-182- echo "Echo spacing should be specified in seconds, not milliseconds. Value of $dwell appears to be incorrectly specified in milliseconds. Try using the value $msdwell instead.";
##############################################
fsl-5.0.8/src/flirt/epi_reg-186- --pedir)
fsl-5.0.8/src/flirt/epi_reg:187: pearg=`get_arg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-188- # These are consistent with the ones used in FUGUE (this has been checked)
##############################################
fsl-5.0.8/src/flirt/epi_reg-203- --weight)
fsl-5.0.8/src/flirt/epi_reg:204: refweight=`get_imarg1 $1`;
fsl-5.0.8/src/flirt/epi_reg-205- use_weighting=yes;
##############################################
fsl-5.0.8/src/flirt/epi_reg-220- *)
fsl-5.0.8/src/flirt/epi_reg:221: #if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then
fsl-5.0.8/src/flirt/epi_reg-222- echo "Unrecognised option $1" 1>&2
##############################################
fsl-5.0.8/src/flirt/epi_reg-295-if [ X$wmseg = X ] ; then
fsl-5.0.8/src/flirt/epi_reg:296: if [ `$FSLDIR/bin/imtest ${vrefbrain}_wmseg` = 0 ] ; then
fsl-5.0.8/src/flirt/epi_reg-297- echo "Running FAST segmentation"
##############################################
fsl-5.0.8/src/flirt/epi_reg-301- for file in ${vrefbrain}_wmseg*; do
fsl-5.0.8/src/flirt/epi_reg:302: absfile=`$FSLDIR/bin/fsl_abspath $file`;
fsl-5.0.8/src/flirt/epi_reg-303- cp ${absfile} ${file/${vrefbrain}_wmseg/${vout}_fast_wmseg} #To link the correct files with extensions
##############################################
fsl-5.0.8/src/flirt/epi_reg-307- # copy specified wmseg file(s)
fsl-5.0.8/src/flirt/epi_reg:308: for file in `$FSLDIR/bin/imglob -extensions ${wmseg}`; do
fsl-5.0.8/src/flirt/epi_reg:309: absfile=`$FSLDIR/bin/fsl_abspath $file`;
fsl-5.0.8/src/flirt/epi_reg-310- cp ${absfile} ${file/${wmseg}/${vout}_fast_wmseg} #To link the correct files with extensions
##############################################
fsl-5.0.8/src/flirt/epi_reg-313-# make a WM edge map for visualisation (good to overlay in FSLView)
fsl-5.0.8/src/flirt/epi_reg:314:if [ `$FSLDIR/bin/imtest ${vrefbrain}_wmedge` = 0 ] ; then
fsl-5.0.8/src/flirt/epi_reg-315- $FSLDIR/bin/fslmaths ${vout}_fast_wmseg -edge -bin -mas ${vout}_fast_wmseg ${vout}_fast_wmedge
##############################################
fsl-5.0.8/src/flirt/epi_reg-317- for file in ${vrefbrain}_wmedge*; do
fsl-5.0.8/src/flirt/epi_reg:318: absfile=`$FSLDIR/bin/fsl_abspath $file`;
fsl-5.0.8/src/flirt/epi_reg-319- cp ${absfile} ${file/${vrefbrain}_wmedge/${vout}_fast_wmedge} #To link the correct files with extensions
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_1_bet-94-mkdir -p struc
fsl-5.0.8/src/fslvbm/fslvbm_1_bet:95:for g in `$FSLDIR/bin/imglob *` ; do
fsl-5.0.8/src/fslvbm/fslvbm_1_bet-96- imcp $g struc/${g}_struc
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_1_bet-100-imagelist=""
fsl-5.0.8/src/fslvbm/fslvbm_1_bet:101:for g in `$FSLDIR/bin/imglob *_struc.*` ; do
fsl-5.0.8/src/fslvbm/fslvbm_1_bet-102- echo $g
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-79-/bin/rm -f fslvbm3a
fsl-5.0.8/src/fslvbm/fslvbm_3_proc:80:for g in `$FSLDIR/bin/imglob *_struc.*` ; do
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-81- echo $g
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-85-chmod a+x fslvbm3a
fsl-5.0.8/src/fslvbm/fslvbm_3_proc:86:fslvbm3a_id=`${FSLDIR}/bin/fsl_sub -T 40 -N fslvbm3a -t ./fslvbm3a`
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-87-echo Doing registrations: ID=$fslvbm3a_id
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-95-
fsl-5.0.8/src/fslvbm/fslvbm_3_proc:96:\$FSLDIR/bin/fslmerge -t GM_merg \`\${FSLDIR}/bin/imglob ../struc/*_GM_to_template_GM.*\`
fsl-5.0.8/src/fslvbm/fslvbm_3_proc:97:\$FSLDIR/bin/fslmerge -t GM_mod_merg \`\${FSLDIR}/bin/imglob ../struc/*_GM_to_template_GM_mod.*\`
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-98-
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-113-
fsl-5.0.8/src/fslvbm/fslvbm_3_proc:114:fslvbm3b_id=`${FSLDIR}/bin/fsl_sub -T 15 -N fslvbm3b -j $fslvbm3a_id ./fslvbm3b`
fsl-5.0.8/src/fslvbm/fslvbm_3_proc-115-
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-97-/bin/rm -f fslvbm2a
fsl-5.0.8/src/fslvbm/fslvbm_2_template:98:for g in `$FSLDIR/bin/imglob *_struc.*` ; do
fsl-5.0.8/src/fslvbm/fslvbm_2_template-99- echo $g
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-103-chmod a+x fslvbm2a
fsl-5.0.8/src/fslvbm/fslvbm_2_template:104:fslvbm2a_id=`$FSLDIR/bin/fsl_sub -T 30 -N fslvbm2a -t ./fslvbm2a`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-105-echo Running segmentation: ID=$fslvbm2a_id
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-108-/bin/rm -f fslvbm2b
fsl-5.0.8/src/fslvbm/fslvbm_2_template:109:for g in `$FSLDIR/bin/imglob *_struc.*` ; do
fsl-5.0.8/src/fslvbm/fslvbm_2_template-110- echo "${FSLDIR}/bin/fsl_reg ${g}_GM $T ${g}_GM_to_T -a" >> fslvbm2b
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-112-chmod a+x fslvbm2b
fsl-5.0.8/src/fslvbm/fslvbm_2_template:113:fslvbm2b_id=`$FSLDIR/bin/fsl_sub -j $fslvbm2a_id -T $HOWLONG -N fslvbm2b -t ./fslvbm2b`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-114-echo Running initial registration: ID=$fslvbm2b_id
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-120- template_list=\`cat ../template_list\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template:121: template_list=\`\$FSLDIR/bin/remove_ext \$template_list\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-122-else
fsl-5.0.8/src/fslvbm/fslvbm_2_template-123- template_list=\`echo *_struc.* | sed 's/_struc\./\./g'\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template:124: template_list=\`\$FSLDIR/bin/remove_ext \$template_list | sort -u\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-125- echo "WARNING - study-specific template will be created from ALL input data - may not be group-size matched!!!"
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-135-chmod +x fslvbm2c
fsl-5.0.8/src/fslvbm/fslvbm_2_template:136:fslvbm2c_id=`fsl_sub -j $fslvbm2b_id -T 15 -N fslvbm2c ./fslvbm2c`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-137-echo Creating first-pass template: ID=$fslvbm2c_id
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-141-T=template_GM_init
fsl-5.0.8/src/fslvbm/fslvbm_2_template:142:for g in `$FSLDIR/bin/imglob *_struc.*` ; do
fsl-5.0.8/src/fslvbm/fslvbm_2_template-143- echo "${FSLDIR}/bin/fsl_reg ${g}_GM $T ${g}_GM_to_T_init $REG -fnirt \"--config=GM_2_MNI152GM_2mm.cnf\"" >> fslvbm2d
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-145-chmod a+x fslvbm2d
fsl-5.0.8/src/fslvbm/fslvbm_2_template:146:fslvbm2d_id=`$FSLDIR/bin/fsl_sub -j $fslvbm2c_id -T $HOWLONG -N fslvbm2d -t ./fslvbm2d`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-147-echo Running registration to first-pass template: ID=$fslvbm2d_id
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-153- template_list=\`cat ../template_list\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template:154: template_list=\`\$FSLDIR/bin/remove_ext \$template_list\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-155-else
fsl-5.0.8/src/fslvbm/fslvbm_2_template-156- template_list=\`echo *_struc.* | sed 's/_struc\./\./g'\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template:157: template_list=\`\$FSLDIR/bin/remove_ext \$template_list | sort -u\`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-158- echo "WARNING - study-specific template will be created from ALL input data - may not be group-size matched!!!"
##############################################
fsl-5.0.8/src/fslvbm/fslvbm_2_template-168-chmod +x fslvbm2e
fsl-5.0.8/src/fslvbm/fslvbm_2_template:169:fslvbm2e_id=`fsl_sub -j $fslvbm2d_id -T 15 -N fslvbm2e ./fslvbm2e`
fsl-5.0.8/src/fslvbm/fslvbm_2_template-170-echo Creating second-pass template: ID=$fslvbm2e_id
##############################################
fsl-5.0.8/src/fast4/lesions-112-
fsl-5.0.8/src/fast4/lesions:113:sizex=`fslval $A pixdim1`
fsl-5.0.8/src/fast4/lesions:114:sizey=`fslval $A pixdim2`
fsl-5.0.8/src/fast4/lesions:115:sizez=`fslval $A pixdim3`
fsl-5.0.8/src/fast4/lesions-116-
fsl-5.0.8/src/fast4/lesions:117:sizex=`echo sqrt \( $sizex ^ 2 \) | bc -l`
fsl-5.0.8/src/fast4/lesions:118:sizey=`echo sqrt \( $sizey ^ 2 \) | bc -l`
fsl-5.0.8/src/fast4/lesions:119:sizez=`echo sqrt \( $sizez ^ 2 \) | bc -l`
fsl-5.0.8/src/fast4/lesions-120-
fsl-5.0.8/src/fast4/lesions-121-min=$sizex
fsl-5.0.8/src/fast4/lesions:122:num=`echo $min/$sizey|bc`
fsl-5.0.8/src/fast4/lesions-123-if [ $num -ge 1 ]; then
##############################################
fsl-5.0.8/src/fast4/lesions-125-fi
fsl-5.0.8/src/fast4/lesions:126:num=`echo $min/$sizez|bc`
fsl-5.0.8/src/fast4/lesions-127-if [ $num -ge 1 ]; then
##############################################
fsl-5.0.8/src/fast4/lesions-129-fi
fsl-5.0.8/src/fast4/lesions:130:num=`echo $min/1.0|bc`
fsl-5.0.8/src/fast4/lesions-131-if [ $num -ge 1 ]; then
##############################################
fsl-5.0.8/src/fast4/lesions-207-
fsl-5.0.8/src/fast4/lesions:208:meanden0=`${FSLDIR}/bin/fslstats ${A}_brain_pve_0 -m`
fsl-5.0.8/src/fast4/lesions-209-${FSLDIR}/bin/fslmaths ${A}_brain_pve_0 -mul ${A}_brain ${A}_multemp -odt float
fsl-5.0.8/src/fast4/lesions:210:meannum0=`${FSLDIR}/bin/fslstats ${A}_multemp -m`
fsl-5.0.8/src/fast4/lesions:211:mean0=`echo $meannum0/$meanden0|bc -l`
fsl-5.0.8/src/fast4/lesions-212-
fsl-5.0.8/src/fast4/lesions:213:meanden1=`${FSLDIR}/bin/fslstats ${A}_brain_pve_1 -m`
fsl-5.0.8/src/fast4/lesions-214-${FSLDIR}/bin/fslmaths ${A}_brain_pve_1 -mul ${A}_brain ${A}_multemp -odt float
fsl-5.0.8/src/fast4/lesions:215:meannum1=`${FSLDIR}/bin/fslstats ${A}_multemp -m`
fsl-5.0.8/src/fast4/lesions:216:mean1=`echo $meannum1/$meanden1|bc -l`
fsl-5.0.8/src/fast4/lesions-217-
fsl-5.0.8/src/fast4/lesions:218:meanden2=`${FSLDIR}/bin/fslstats ${A}_brain_pve_2 -m`
fsl-5.0.8/src/fast4/lesions-219-${FSLDIR}/bin/fslmaths ${A}_brain_pve_2 -mul ${A}_brain ${A}_multemp -odt float
fsl-5.0.8/src/fast4/lesions:220:meannum2=`${FSLDIR}/bin/fslstats ${A}_multemp -m`
fsl-5.0.8/src/fast4/lesions:221:mean2=`echo $meannum2/$meanden2|bc -l`
fsl-5.0.8/src/fast4/lesions-222-
fsl-5.0.8/src/fast4/lesions:223:#denom=`echo $mean0+$mean2|bc`
fsl-5.0.8/src/fast4/lesions:224:num2=`echo $mean1|bc -l`
fsl-5.0.8/src/fast4/lesions:225:num1=`echo $hypoparam/1.0|bc`
fsl-5.0.8/src/fast4/lesions-226-if [ $num1 -lt 1 ]; then
fsl-5.0.8/src/fast4/lesions:227: num2=`echo $mean0-$hypoparam*$mean0+$mean1*$hypoparam|bc -l`;
fsl-5.0.8/src/fast4/lesions-228-fi
fsl-5.0.8/src/fast4/lesions-229-if [ $num1 -ge 1 ]; then
fsl-5.0.8/src/fast4/lesions:230: num2=`echo $hypoparam*$mean2-$hypoparam*$mean1+2.0*$mean1-$mean2|bc -l`;
fsl-5.0.8/src/fast4/lesions-231-fi
##############################################
fsl-5.0.8/src/fast4/lesions-242-
fsl-5.0.8/src/fast4/lesions:243:echo `${FSLDIR}/bin/fslstats ${A}_lesions -m -v | awk '{print "2 k " $1 " " $3 " * 1000 / p" }' | dc -` > ${A}_lesions.txt
fsl-5.0.8/src/fast4/lesions:244:echo "$A `cat ${A}_lesions.txt`"
fsl-5.0.8/src/fast4/lesions-245-
##############################################
fsl-5.0.8/src/feat5/fslerrorreport-73-
fsl-5.0.8/src/feat5/fslerrorreport:74:filename=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/feat5/fslerrorreport-75-if [ "X$filename" = X ] ; then
##############################################
fsl-5.0.8/src/feat5/fslerrorreport-137-
fsl-5.0.8/src/feat5/fslerrorreport:138:if [ `echo $imgname | grep \.feat | wc -l` -ge 1 ] ; then
fsl-5.0.8/src/feat5/fslerrorreport-139- featname=$imgname
##############################################
fsl-5.0.8/src/feat5/fslerrorreport-141-fi
fsl-5.0.8/src/feat5/fslerrorreport:142:if [ `echo $imgname | grep \.gfeat | wc -l` -ge 1 ] ; then
fsl-5.0.8/src/feat5/fslerrorreport-143- featname=$imgname
##############################################
fsl-5.0.8/src/feat5/fslerrorreport-145-fi
fsl-5.0.8/src/feat5/fslerrorreport:146:if [ `echo $imgname | grep \.bedpost | wc -l` -ge 1 ] ; then
fsl-5.0.8/src/feat5/fslerrorreport-147- fdtname=$imgname
##############################################
fsl-5.0.8/src/feat5/fslerrorreport-149-fi
fsl-5.0.8/src/feat5/fslerrorreport:150:if [ `echo $imgname | grep \.ica | wc -l` -ge 1 ] ; then
fsl-5.0.8/src/feat5/fslerrorreport-151- icaname=$imgname
##############################################
fsl-5.0.8/src/feat5/renderhighres-90-
fsl-5.0.8/src/feat5/renderhighres:91:if [ `${FSLDIR}/bin/imtest reg/$space` != 1 ] ; then
fsl-5.0.8/src/feat5/renderhighres-92- echo "Can't use $space for output space - doesn't exist in the FEAT registration output"
##############################################
fsl-5.0.8/src/feat5/renderhighres-95-
fsl-5.0.8/src/feat5/renderhighres:96:if [ `${FSLDIR}/bin/imtest reg/$background` != 1 ] ; then
fsl-5.0.8/src/feat5/renderhighres-97- echo "Can't use $background for background image - doesn't exist in the FEAT registration output"
##############################################
fsl-5.0.8/src/feat5/renderhighres-105-if [ $background != $space ] ; then
fsl-5.0.8/src/feat5/renderhighres:106: if [ `${FSLDIR}/bin/imtest ../reg/highres2standard_warp` = 1 ] ; then
fsl-5.0.8/src/feat5/renderhighres-107- if [ $background = standard ] ; then
##############################################
fsl-5.0.8/src/feat5/renderhighres-119-
fsl-5.0.8/src/feat5/renderhighres:120:for f in `cd .. ; ${FSLDIR}/bin/imglob thresh_*.*` ; do
fsl-5.0.8/src/feat5/renderhighres:121: f=`${FSLDIR}/bin/remove_ext $f`
fsl-5.0.8/src/feat5/renderhighres-122-
fsl-5.0.8/src/feat5/renderhighres:123: if [ $space = standard ] && [ `${FSLDIR}/bin/imtest ../reg/highres2standard_warp` = 1 ] ; then
fsl-5.0.8/src/feat5/renderhighres-124- ${FSLDIR}/bin/applywarp --ref=../reg/standard --in=../$f --out=$f --warp=../reg/highres2standard_warp --premat=../reg/example_func2highres.mat --interp=spline
##############################################
fsl-5.0.8/src/feat5/renderhighres-129- if [ $autothresh = 1 ] ; then
fsl-5.0.8/src/feat5/renderhighres:130: minZ=`${FSLDIR}/bin/fslstats ../$f -l 0.01 -R | awk '{print $1}'`
fsl-5.0.8/src/feat5/renderhighres:131: maxZ=`${FSLDIR}/bin/fslstats ../$f -R | awk '{print $2}'`
fsl-5.0.8/src/feat5/renderhighres-132- else
##############################################
fsl-5.0.8/src/feat5/feat_gm_prepare-85-
fsl-5.0.8/src/feat5/feat_gm_prepare:86:OUT=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/feat5/feat_gm_prepare-87-shift
##############################################
fsl-5.0.8/src/feat5/feat_gm_prepare-90-echo Estimating smoothness of functional data...
fsl-5.0.8/src/feat5/feat_gm_prepare:91:func_smoothing=`grep "fmri(smooth)" $1/design.fsf | tail -n 1 | awk '{print $3}'`
fsl-5.0.8/src/feat5/feat_gm_prepare:92:standard_space_resolution=`${FSLDIR}/bin/fslval $1/reg/standard pixdim1`
fsl-5.0.8/src/feat5/feat_gm_prepare:93:struc_smoothing=`${FSLDIR}/bin/match_smoothing $1/example_func $func_smoothing $1/reg/highres $standard_space_resolution`
fsl-5.0.8/src/feat5/feat_gm_prepare-94-echo Structural-space GM PVE images will be smoothed by sigma=${struc_smoothing}mm to match the standard-space functional data
##############################################
fsl-5.0.8/src/feat5/feat_gm_prepare-101- ${FSLDIR}/bin/fslecho "cd ${f}/reg; $FSLDIR/bin/fast -R 0.3 -H 0.1 -o grot highres; $FSLDIR/bin/immv grot_pve_1 highresGM; /bin/rm grot*; $FSLDIR/bin/fslmaths highresGM -s $struc_smoothing highresGMs; \c" >> ${OUT}.log/featseg1
fsl-5.0.8/src/feat5/feat_gm_prepare:102: if [ `${FSLDIR}/bin/imtest ${f}/reg/highres2standard_warp` = 1 ] ; then
fsl-5.0.8/src/feat5/feat_gm_prepare-103- ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/applywarp --ref=standard --in=highresGMs --out=highresGMs2standard --warp=highres2standard_warp; \c" >> ${OUT}.log/featseg1
##############################################
fsl-5.0.8/src/feat5/feat_gm_prepare-111-echo Running segmentations...
fsl-5.0.8/src/feat5/feat_gm_prepare:112:featseg1_id=`$FSLDIR/bin/fsl_sub -T 30 -N featseg1 -l ./${OUT}.log -t ./${OUT}.log/featseg1`
fsl-5.0.8/src/feat5/feat_gm_prepare-113-
##############################################
fsl-5.0.8/src/feat5/setFEAT-70-Usage() {
fsl-5.0.8/src/feat5/setFEAT:71: function=`basename $0`
fsl-5.0.8/src/feat5/setFEAT-72- echo Command-line editing of FSL design .\*fsf files
##############################################
fsl-5.0.8/src/feat5/setFEAT-132-shiftpos() {
fsl-5.0.8/src/feat5/setFEAT:133: eval "pos=`echo $pos+1 | bc`"
fsl-5.0.8/src/feat5/setFEAT-134-}
##############################################
fsl-5.0.8/src/feat5/setFEAT-137-
fsl-5.0.8/src/feat5/setFEAT:138:firstchar=`echo $1 | head -c 1`
fsl-5.0.8/src/feat5/setFEAT-139-if [[ $firstchar == '-' ]]
fsl-5.0.8/src/feat5/setFEAT-140-then shift
fsl-5.0.8/src/feat5/setFEAT:141: firstchar=`echo $1 | head -c 1`
fsl-5.0.8/src/feat5/setFEAT-142-
##############################################
fsl-5.0.8/src/feat5/setFEAT-145- shift
fsl-5.0.8/src/feat5/setFEAT:146: firstchar=`echo $1 | head -c 1`
fsl-5.0.8/src/feat5/setFEAT-147- done
##############################################
fsl-5.0.8/src/feat5/setFEAT-162- cp $input $fsffile
fsl-5.0.8/src/feat5/setFEAT:163: fsffile=`cat $fsffile`
fsl-5.0.8/src/feat5/setFEAT:164: outfsffile=`echo $outputdirs | awk '{print $'$cnt'}'`
fsl-5.0.8/src/feat5/setFEAT:165: cnt=`echo $cnt + 1 | bc`
fsl-5.0.8/src/feat5/setFEAT-166- tempname=`tmpnam`
##############################################
fsl-5.0.8/src/feat5/setFEAT-262-
fsl-5.0.8/src/feat5/setFEAT:263: npts=`echo "$fsffile" | grep -o 'npts).*' | sed 's/npts) //'`
fsl-5.0.8/src/feat5/setFEAT-264-
fsl-5.0.8/src/feat5/setFEAT:265: for a in `seq $in2`; do
fsl-5.0.8/src/feat5/setFEAT-266- # Check if EVs exist
##############################################
fsl-5.0.8/src/feat5/setFEAT-271- # Set orthogonalisation, EB
fsl-5.0.8/src/feat5/setFEAT:272: for b in `seq $in2`;do
fsl-5.0.8/src/feat5/setFEAT-273- # Check if orth exists:
##############################################
fsl-5.0.8/src/feat5/setFEAT-285- then
fsl-5.0.8/src/feat5/setFEAT:286: lineno=`echo "$fsffile" | grep -n "evg.*\.$a)" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-287- else
fsl-5.0.8/src/feat5/setFEAT:288: lineno=`echo "$fsffile" | wc -l | sed 's/ .*//'`
fsl-5.0.8/src/feat5/setFEAT-289- fi
##############################################
fsl-5.0.8/src/feat5/setFEAT-296- # Set EV values to 0
fsl-5.0.8/src/feat5/setFEAT:297: for b in `seq $npts`;do
fsl-5.0.8/src/feat5/setFEAT-298- # Check if EV exists
##############################################
fsl-5.0.8/src/feat5/setFEAT-310- then
fsl-5.0.8/src/feat5/setFEAT:311: lineno=`echo "$fsffile" | grep -n "evg.*\.$a)" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-312- else
fsl-5.0.8/src/feat5/setFEAT:313: lineno=`echo "$fsffile" | wc -l | sed 's/ .*//'`
fsl-5.0.8/src/feat5/setFEAT-314- fi
##############################################
fsl-5.0.8/src/feat5/setFEAT-358- # Set orthogonalisation, EB
fsl-5.0.8/src/feat5/setFEAT:359: for b in `seq $in2`;do
fsl-5.0.8/src/feat5/setFEAT-360- txt=$txt"# Orthogonalise EV $a wrt EV $b\n\n"
##############################################
fsl-5.0.8/src/feat5/setFEAT-365-
fsl-5.0.8/src/feat5/setFEAT:366: lastev=`echo $a-1 | bc`
fsl-5.0.8/src/feat5/setFEAT-367-
##############################################
fsl-5.0.8/src/feat5/setFEAT-369- then
fsl-5.0.8/src/feat5/setFEAT:370: lineno=`echo "$fsffile" | grep -n "evg.*\.$lastev)" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-371- elif echo "$fsffile" | grep -q "confoundevs" ;
fsl-5.0.8/src/feat5/setFEAT-372- then
fsl-5.0.8/src/feat5/setFEAT:373: lineno=`echo "$fsffile" | grep -n "confoundevs" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-374- else
fsl-5.0.8/src/feat5/setFEAT:375: lineno=`echo "$fsffile" | wc -l | sed 's/ .*//'`
fsl-5.0.8/src/feat5/setFEAT-376- fi
##############################################
fsl-5.0.8/src/feat5/setFEAT-384- # Set EV values to 0
fsl-5.0.8/src/feat5/setFEAT:385: for b in `seq $npts`;do
fsl-5.0.8/src/feat5/setFEAT-386- txt=$txt"# Higher-level EV value for EV $a and input $b\n\n"
##############################################
fsl-5.0.8/src/feat5/setFEAT-391-
fsl-5.0.8/src/feat5/setFEAT:392: lastev=`echo $a-1 | bc`
fsl-5.0.8/src/feat5/setFEAT-393-
##############################################
fsl-5.0.8/src/feat5/setFEAT-395- then
fsl-5.0.8/src/feat5/setFEAT:396: lineno=`echo "$fsffile" | grep -n "evg.*\.$lastev)" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-397- elif echo "$fsffile" | grep -q "confoundevs" ;
fsl-5.0.8/src/feat5/setFEAT-398- then
fsl-5.0.8/src/feat5/setFEAT:399: lineno=`echo "$fsffile" | grep -n "confoundevs" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-400- else
fsl-5.0.8/src/feat5/setFEAT:401: lineno=`echo "$fsffile" | wc -l | sed 's/ .*//'`
fsl-5.0.8/src/feat5/setFEAT-402- fi
##############################################
fsl-5.0.8/src/feat5/setFEAT-500- then
fsl-5.0.8/src/feat5/setFEAT:501: lineno=`echo "$fsffile" | grep -n "deriv_yn$2)" | tail -n 1 | sed 's/:.*//'`
fsl-5.0.8/src/feat5/setFEAT-502- else
fsl-5.0.8/src/feat5/setFEAT:503: lineno=`echo "$fsffile" | wc -l | sed 's/ .*//'`
fsl-5.0.8/src/feat5/setFEAT-504- fi
##############################################
fsl-5.0.8/src/feat5/setFEAT-674- then
fsl-5.0.8/src/feat5/setFEAT:675: # dir=`echo "$fsffile" | grep outputdir | sed 's/[^"]*"\([^"]*\)"/\1/g'`
fsl-5.0.8/src/feat5/setFEAT:676: dir=`echo "$fsffile" | grep outputdir | awk '{ print $NF }'`
fsl-5.0.8/src/feat5/setFEAT-677-
fsl-5.0.8/src/feat5/setFEAT:678: firstchar=`echo $dir | head -c 1`
fsl-5.0.8/src/feat5/setFEAT:679: lastchar=`echo $dir | tail -c 1`
fsl-5.0.8/src/feat5/setFEAT-680-
##############################################
fsl-5.0.8/src/feat5/setFEAT-684- then newdir=$dir/$in2
fsl-5.0.8/src/feat5/setFEAT:685: else newdir=`dirname $dir`/$in2
fsl-5.0.8/src/feat5/setFEAT:686: newdir=`echo $newdir | sed 's/^.\//\//g'`
fsl-5.0.8/src/feat5/setFEAT-687- fi
##############################################
fsl-5.0.8/src/feat5/setFEAT-696- ## not working
fsl-5.0.8/src/feat5/setFEAT:697: dir=`cat "$fsffile" | grep feat_files\(1\) | sed 's/[^"]*"\([^"]*\)"/\1/g'`
fsl-5.0.8/src/feat5/setFEAT-698-
fsl-5.0.8/src/feat5/setFEAT:699: firstchar=`echo $dir | head -c 1`
fsl-5.0.8/src/feat5/setFEAT:700: lastchar=`echo $dir | tail -c 1`
fsl-5.0.8/src/feat5/setFEAT-701- if [[ $dir == '' ]]
##############################################
fsl-5.0.8/src/feat5/setFEAT-704- then newdir=$dir/$in2
fsl-5.0.8/src/feat5/setFEAT:705: else newdir=`dirname $dir`/$in2
fsl-5.0.8/src/feat5/setFEAT-706- newdir=$(echo $newdir | sed 's/^.\///g')
##############################################
fsl-5.0.8/src/feat5/setFEAT-720-
fsl-5.0.8/src/feat5/setFEAT:721: npts=`fslval $in3 dim4 | grep -o "[0-9.]*"`
fsl-5.0.8/src/feat5/setFEAT:722: TR=`fslval $in3 pixdim4 | grep -o "[0-9.]*"`
fsl-5.0.8/src/feat5/setFEAT-723-
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-72-usage() {
fsl-5.0.8/src/feat5/mainfeatreg:73: echo "Usage: `basename $0` <feat_directory> [-pngs]"
fsl-5.0.8/src/feat5/mainfeatreg-74- echo "-a <file> fieldmap image ( for unwarping ). Also enables unwarping mode"
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-108-writeToFile $1 0 1 "\n$2"
fsl-5.0.8/src/feat5/mainfeatreg:109:output=`sh -c "$2"`
fsl-5.0.8/src/feat5/mainfeatreg-110-if [ x$1 != x ]
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-114-fi
fsl-5.0.8/src/feat5/mainfeatreg:115:output=`echo $output | tail -n 1`
fsl-5.0.8/src/feat5/mainfeatreg-116-if [ "${3}" != "" ]
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-177-
fsl-5.0.8/src/feat5/mainfeatreg:178:thresh50=`awk "BEGIN {print $thresh50 / 2.0}"`
fsl-5.0.8/src/feat5/mainfeatreg-179-runCommand $1 "${FSLDIR}/bin/fslmaths FM_UD_fmap_mag_brain -thr $thresh50 -bin FM_UD_fmap_mag_brain_mask50"
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-203-# get a sigloss estimate and make a siglossed mag for forward warp
fsl-5.0.8/src/feat5/mainfeatreg:204:epi_te=`awk "BEGIN {print $echoTime / 1000.0}"`
fsl-5.0.8/src/feat5/mainfeatreg-205-runCommand $1 "${FSLDIR}/bin/sigloss -i FM_UD_fmap --te=$epi_te -m FM_UD_fmap_mag_brain_mask -s FM_UD_fmap_sigloss"
fsl-5.0.8/src/feat5/mainfeatreg:206:siglossthresh=`awk "BEGIN {print 1.0 - ( $signalLossThreshold / 100.0 )}"`
fsl-5.0.8/src/feat5/mainfeatreg-207-runCommand $1 "${FSLDIR}/bin/fslmaths FM_UD_fmap_sigloss -mul FM_UD_fmap_mag_brain FM_UD_fmap_mag_brain_siglossed -odt float"
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-230-#Check for existing registrations
fsl-5.0.8/src/feat5/mainfeatreg:231: if [ `${FSLDIR}/bin/imtest ${1}2${2}_warp` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-232- then runCommand $9 "${FSLDIR}/bin/applywarp --ref=$2 --in=$1 --out=$out --warp=${1}2${2}_warp"
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-244- then
fsl-5.0.8/src/feat5/mainfeatreg:245: echoSpacingSeconds=`awk "BEGIN {print $echoSpacing / 1000}"`
fsl-5.0.8/src/feat5/mainfeatreg-246- runCommand $9 "${FSLDIR}/bin/epi_reg --epi=$1 --t1=$2_head --t1brain=$2 --out=$out --fmap=unwarp/FM_UD_fmap --fmapmag=unwarp/FM_UD_fmap_mag --fmapmagbrain=unwarp/FM_UD_fmap_mag_brain --echospacing=$echoSpacingSeconds --pedir=$phaseEncodingDirection"
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-252- runCommand $9 "${FSLDIR}/bin/fslstats FM_UD_fmap2epi_shift -R -P 1 -P 99" shiftminmax
fsl-5.0.8/src/feat5/mainfeatreg:253: shiftminR=`echo $shiftminmax | awk {'print $1'}`
fsl-5.0.8/src/feat5/mainfeatreg:254: shiftmaxR=`echo $shiftminmax | awk {'print $2'}`
fsl-5.0.8/src/feat5/mainfeatreg:255: shiftminr=`echo $shiftminmax | awk {'print $3'}`
fsl-5.0.8/src/feat5/mainfeatreg:256: shiftminr=`awk "BEGIN {print $shiftminr * -1.0}"`
fsl-5.0.8/src/feat5/mainfeatreg:257: shiftmaxr=`echo $shiftminmax | awk {'print $4'}`
fsl-5.0.8/src/feat5/mainfeatreg-258-
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-493-
fsl-5.0.8/src/feat5/mainfeatreg:494:if [ `${FSLDIR}/bin/imtest example_func` = 0 ]
fsl-5.0.8/src/feat5/mainfeatreg-495- then ${FSLDIR}/bin/imcp $inputImage example_func
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-514-
fsl-5.0.8/src/feat5/mainfeatreg:515: if [ `${FSLDIR}/bin/imtest $magnitudeImage` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-516- then
fsl-5.0.8/src/feat5/mainfeatreg:517: runCommand $logFile "${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/remove_ext $magnitudeImage` FM_UD_fmap_mag_brain"
fsl-5.0.8/src/feat5/mainfeatreg-518-
fsl-5.0.8/src/feat5/mainfeatreg-519- magnitudeHead=${magnitudeImage/_brain/}
fsl-5.0.8/src/feat5/mainfeatreg:520: if [ `${FSLDIR}/bin/imtest $magnitudeHead` != 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-521- then magnitudeHead=$magnitudeImage
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-525- runCommand $logFile "${FSLDIR}/bin/fslstats FM_UD_fmap_mag_brain -v | awk '{ print \$1 }'" nvox
fsl-5.0.8/src/feat5/mainfeatreg:526: frac_nzvox=`awk "BEGIN {print $nzvox / $nvox}"`
fsl-5.0.8/src/feat5/mainfeatreg-527- writeToFile $logFile 0 1 "$frac_nzvox"
fsl-5.0.8/src/feat5/mainfeatreg:528: if [ `expr $frac_nzvox \> 0.9` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-529- then
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-538-
fsl-5.0.8/src/feat5/mainfeatreg:539:if [ `${FSLDIR}/bin/imtest ./unwarp/EF_UD_fmap_sigloss` = 1 ] # test for weighting image from fieldmap unwarping to use with example_func
fsl-5.0.8/src/feat5/mainfeatreg-540- then
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-546-
fsl-5.0.8/src/feat5/mainfeatreg:547:if [ `${FSLDIR}/bin/imtest $initialHighresImage` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-548- then
fsl-5.0.8/src/feat5/mainfeatreg:549: runCommand $logFile "${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/remove_ext $initialHighresImage` initial_highres"
fsl-5.0.8/src/feat5/mainfeatreg-550- else if [ "$initialHighresImage" != "" ]
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-558-
fsl-5.0.8/src/feat5/mainfeatreg:559:if [ `${FSLDIR}/bin/imtest $highresImage` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-560- then
fsl-5.0.8/src/feat5/mainfeatreg:561: runCommand $logFile "${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/remove_ext $highresImage` highres"
fsl-5.0.8/src/feat5/mainfeatreg-562- if [ "$nonLinearResolution" != "" -o $highresDof = "BBR" ]
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-564- highresHead=${highresImage/_brain/}
fsl-5.0.8/src/feat5/mainfeatreg:565: if [ `${FSLDIR}/bin/imtest $highresHead` != 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-566- then highresHead=$highresImage
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-569- highresSegmentationRoot=${highresImage/_brain/}
fsl-5.0.8/src/feat5/mainfeatreg:570: if [ `${FSLDIR}/bin/imtest ${highresSegmentationRoot}_brain_wmseg` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-571- then
fsl-5.0.8/src/feat5/mainfeatreg-572- runCommand $logFile "${FSLDIR}/bin/fslmaths ${highresSegmentationRoot}_brain_wmseg highres_wmseg"
fsl-5.0.8/src/feat5/mainfeatreg:573: elif [ `${FSLDIR}/bin/imtest ${highresSegmentationRoot}_wmseg` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-574- then
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-586-
fsl-5.0.8/src/feat5/mainfeatreg:587:if [ `${FSLDIR}/bin/imtest $standardImage` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-588- then
fsl-5.0.8/src/feat5/mainfeatreg:589: runCommand $logFile "${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/remove_ext $standardImage` standard"
fsl-5.0.8/src/feat5/mainfeatreg-590- if [ "$nonLinearResolution" != "" ]
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-592- standardHead=${standardImage/_brain/}
fsl-5.0.8/src/feat5/mainfeatreg:593: if [ `${FSLDIR}/bin/imtest $standardHead` != 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-594- then standardHead=$standardImage
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-596- runCommand $logFile "${FSLDIR}/bin/fslmaths $standardHead standard_head"
fsl-5.0.8/src/feat5/mainfeatreg:597: standardMaskName=`${FSLDIR}/bin/remove_ext $standardImage`_mask_dil
fsl-5.0.8/src/feat5/mainfeatreg:598: if [ `${FSLDIR}/bin/imtest $standardMaskName` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-599- then
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-607-#Do registrations:
fsl-5.0.8/src/feat5/mainfeatreg:608:if [ `${FSLDIR}/bin/imtest initial_highres` = 0 -a `${FSLDIR}/bin/imtest highres` = 0 -a `${FSLDIR}/bin/imtest standard` = 0 ]
fsl-5.0.8/src/feat5/mainfeatreg-609- then
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-611- exit 1
fsl-5.0.8/src/feat5/mainfeatreg:612:elif [ `${FSLDIR}/bin/imtest highres` = 0 ] # $1 in $2 ref $3 dof $4 search $5 interp $6 report $7 in_weighting $8 nonlinearwarpres $9 logfile
fsl-5.0.8/src/feat5/mainfeatreg-613- then runFlirt example_func standard $standardDof $standardSearch trilinear $htmlReport "$ef_weighting_flag" "" $logFile ""
fsl-5.0.8/src/feat5/mainfeatreg:614:elif [ `${FSLDIR}/bin/imtest initial_highres` = 0 ]
fsl-5.0.8/src/feat5/mainfeatreg-615- then runFlirt example_func highres $highresDof $highresSearch trilinear $htmlReport "$ef_weighting_flag" "" $logFile "" #need to signal BBR
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-619-fi
fsl-5.0.8/src/feat5/mainfeatreg:620:if [ `${FSLDIR}/bin/imtest highres` = 1 -a `${FSLDIR}/bin/imtest standard` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-621- then runFlirt highres standard $standardDof $standardSearch trilinear $htmlReport "" "$nonLinearResolution" $logFile $fnirtConfig
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-624-#Do missing upscales
fsl-5.0.8/src/feat5/mainfeatreg:625:if [ `${FSLDIR}/bin/imtest highres` = 1 -a `${FSLDIR}/bin/imtest initial_highres` = 1 ] #Then we must have an initialHighresImage present
fsl-5.0.8/src/feat5/mainfeatreg-626- then
fsl-5.0.8/src/feat5/mainfeatreg-627- runCommand $logFile "${FSLDIR}/bin/convert_xfm -omat example_func2highres.mat -concat initial_highres2highres.mat example_func2initial_highres.mat"
fsl-5.0.8/src/feat5/mainfeatreg:628: if [ `${FSLDIR}/bin/imtest initial_highres2highres_warp` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-629- then
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-635-fi
fsl-5.0.8/src/feat5/mainfeatreg:636:if [ `${FSLDIR}/bin/imtest standard` = 1 -a `${FSLDIR}/bin/imtest highres` = 1 ] #Then we must have an highresImage present
fsl-5.0.8/src/feat5/mainfeatreg-637- then
fsl-5.0.8/src/feat5/mainfeatreg-638- runCommand $logFile "${FSLDIR}/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat"
fsl-5.0.8/src/feat5/mainfeatreg:639: if [ `${FSLDIR}/bin/imtest highres2standard_warp` = 1 ] #Nonlinear registation occured
fsl-5.0.8/src/feat5/mainfeatreg-640- then runCommand $logFile "${FSLDIR}/bin/convertwarp --ref=standard --premat=example_func2highres.mat --warp1=highres2standard_warp --out=example_func2standard_warp"
##############################################
fsl-5.0.8/src/feat5/mainfeatreg-644-#Now replace the original TOP level example func with the undistorted version, and save the original distorted version
fsl-5.0.8/src/feat5/mainfeatreg:645:if [ `${FSLDIR}/bin/imtest example_func2highres_warp` = 1 ]
fsl-5.0.8/src/feat5/mainfeatreg-646- then
##############################################
fsl-5.0.8/src/feat5/pnm_stage1-72-usage() {
fsl-5.0.8/src/feat5/pnm_stage1:73: echo "Usage: `basename $0` [popp options]"
fsl-5.0.8/src/feat5/pnm_stage1-74- echo " Runs popp (see options below) and then creates necessary scripts"
##############################################
fsl-5.0.8/src/feat5/pnm_stage1-90- if [ $1 = "-o" ] ; then obase=$2; fi
fsl-5.0.8/src/feat5/pnm_stage1:91: if [ X`echo $1 | grep -- --out=` != X ] ; then obase=`echo $1 | sed 's/--out=//'`; fi
fsl-5.0.8/src/feat5/pnm_stage1-92- shift;
fsl-5.0.8/src/feat5/pnm_stage1-93-done
fsl-5.0.8/src/feat5/pnm_stage1:94:obase=`$FSLDIR/bin/fsl_abspath $obase`;
fsl-5.0.8/src/feat5/pnm_stage1-95-
##############################################
fsl-5.0.8/src/feat5/pnm_stage1-100-jsdata=${obase}_pnm.js
fsl-5.0.8/src/feat5/pnm_stage1:101:odir=`dirname $obase`;
fsl-5.0.8/src/feat5/pnm_stage1:102:odir=`$FSLDIR/bin/fsl_abspath $odir`;
fsl-5.0.8/src/feat5/pnm_stage1-103-
##############################################
fsl-5.0.8/src/feat5/pnm_stage1-123-browser_comm=firefox
fsl-5.0.8/src/feat5/pnm_stage1:124:if [ X`echo $FSLMACHTYPE | grep apple` != X ] ; then
fsl-5.0.8/src/feat5/pnm_stage1-125- browser_comm='open -a Firefox';
##############################################
fsl-5.0.8/src/feat5/estnoise-77-[ "$1" = "" ] && Usage
fsl-5.0.8/src/feat5/estnoise:78:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/feat5/estnoise-79-
##############################################
fsl-5.0.8/src/feat5/estnoise-84-
fsl-5.0.8/src/feat5/estnoise:85:IN=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/feat5/estnoise:86:TMP=`${FSLDIR}/bin/tmpnam /tmp/estnoise`
fsl-5.0.8/src/feat5/estnoise-87-
##############################################
fsl-5.0.8/src/feat5/estnoise-103-# get median non-background value from noise and ar1 images
fsl-5.0.8/src/feat5/estnoise:104:noise=`${FSLDIR}/bin/fslstats ${TMP}_noise -P 50`
fsl-5.0.8/src/feat5/estnoise:105:ar=`${FSLDIR}/bin/fslstats ${TMP}_ar1 -P 50`
fsl-5.0.8/src/feat5/estnoise-106-echo $noise $ar
##############################################
fsl-5.0.8/src/feat5/match_smoothing-80- # resample to required resolution
fsl-5.0.8/src/feat5/match_smoothing:81: XDIM=`${FSLDIR}/bin/fslval $IN dim1`
fsl-5.0.8/src/feat5/match_smoothing:82: YDIM=`${FSLDIR}/bin/fslval $IN dim2`
fsl-5.0.8/src/feat5/match_smoothing:83: ZDIM=`${FSLDIR}/bin/fslval $IN dim3`
fsl-5.0.8/src/feat5/match_smoothing:84: XPIXDIM=`${FSLDIR}/bin/fslval $IN pixdim1`
fsl-5.0.8/src/feat5/match_smoothing:85: YPIXDIM=`${FSLDIR}/bin/fslval $IN pixdim2`
fsl-5.0.8/src/feat5/match_smoothing:86: ZPIXDIM=`${FSLDIR}/bin/fslval $IN pixdim3`
fsl-5.0.8/src/feat5/match_smoothing:87: NEWXDIM=`echo "$XDIM 1 - $XPIXDIM * $NEWRES / p" | dc -`
fsl-5.0.8/src/feat5/match_smoothing:88: NEWYDIM=`echo "$YDIM 1 - $YPIXDIM * $NEWRES / p" | dc -`
fsl-5.0.8/src/feat5/match_smoothing:89: NEWZDIM=`echo "$ZDIM 1 - $ZPIXDIM * $NEWRES / p" | dc -`
fsl-5.0.8/src/feat5/match_smoothing-90- ${FSLDIR}/bin/fslcreatehd $NEWXDIM $NEWYDIM $NEWZDIM 1 $NEWRES $NEWRES $NEWRES 1 0 0 0 16 ${IN}_new
##############################################
fsl-5.0.8/src/feat5/match_smoothing-94- ${FSLDIR}/bin/fslmaths ${IN}_new -mul 0 -add 1 ${IN}_new_mask
fsl-5.0.8/src/feat5/match_smoothing:95: smoothness=`${FSLDIR}/bin/smoothest -z ${IN}_new -m ${IN}_new_mask | tail -n 1 | awk '{print $2}'`
fsl-5.0.8/src/feat5/match_smoothing-96-}
##############################################
fsl-5.0.8/src/feat5/match_smoothing-107-FUNC=$1
fsl-5.0.8/src/feat5/match_smoothing:108:FUNCSMOOTH=`echo "10 k $2 2.355 / p" | dc -`
fsl-5.0.8/src/feat5/match_smoothing-109-STRUC=$3
##############################################
fsl-5.0.8/src/feat5/match_smoothing-111-
fsl-5.0.8/src/feat5/match_smoothing:112:tmp=`${FSLDIR}/bin/tmpnam`
fsl-5.0.8/src/feat5/match_smoothing-113-/bin/rm $tmp # remove empty tmp file
##############################################
fsl-5.0.8/src/feat5/match_smoothing-124-SMOOTH_HIGH=20
fsl-5.0.8/src/feat5/match_smoothing:125:while [ `echo "$SMOOTH $SMOOTH_LAST - $SMOOTH $SMOOTH_LAST - * 100 * 1 / p" | dc -` -ne 0 ] ; do
fsl-5.0.8/src/feat5/match_smoothing-126- SMOOTH_LAST=$SMOOTH
##############################################
fsl-5.0.8/src/feat5/match_smoothing-128- #echo Smoothing structural by $SMOOTH gives 1 resel = $smoothness standard-space voxels
fsl-5.0.8/src/feat5/match_smoothing:129: if [ `echo "$smoothness $func_smoothness - 1 / p" | dc -` -le 0 ] ; then
fsl-5.0.8/src/feat5/match_smoothing-130- SMOOTH_LOW=$SMOOTH
fsl-5.0.8/src/feat5/match_smoothing:131: SMOOTH=`echo "2 k $SMOOTH_HIGH $SMOOTH - 2 / $SMOOTH + p" | dc -`
fsl-5.0.8/src/feat5/match_smoothing-132- else
fsl-5.0.8/src/feat5/match_smoothing-133- SMOOTH_HIGH=$SMOOTH
fsl-5.0.8/src/feat5/match_smoothing:134: SMOOTH=`echo "2 k $SMOOTH $SMOOTH_LOW - 2 / $SMOOTH_LOW + p" | dc -`
fsl-5.0.8/src/feat5/match_smoothing-135- fi
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-74-{
fsl-5.0.8/src/feat5/fsl_motion_outliers:75: echo "Usage: `basename $0` -i <input 4D image> -o <output confound file> [options]"
fsl-5.0.8/src/feat5/fsl_motion_outliers:76: echo " (old version) `basename $0` <unfiltered 4D image> <number of dummy scans> <output confound file>"
fsl-5.0.8/src/feat5/fsl_motion_outliers-77- echo " "
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-95-get_opt1() {
fsl-5.0.8/src/feat5/fsl_motion_outliers:96: arg=`echo $1 | sed 's/=.*//'`
fsl-5.0.8/src/feat5/fsl_motion_outliers-97- echo $arg
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-101-get_arg1() {
fsl-5.0.8/src/feat5/fsl_motion_outliers:102: if [ X`echo $1 | grep '='` = X ] ; then
fsl-5.0.8/src/feat5/fsl_motion_outliers-103- echo "Option $1 requires an argument" 1>&2
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-105- else
fsl-5.0.8/src/feat5/fsl_motion_outliers:106: arg=`echo $1 | sed 's/.*=//'`
fsl-5.0.8/src/feat5/fsl_motion_outliers-107- if [ X$arg = X ] ; then
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-143-while [ $# -ge 1 ] ; do
fsl-5.0.8/src/feat5/fsl_motion_outliers:144: niter=`echo $niter + 1 | bc`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:145: iarg=`get_opt1 $1`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-146- case "$iarg"
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-148- -i)
fsl-5.0.8/src/feat5/fsl_motion_outliers:149: mcf=`get_arg2 $1 $2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-150- shift 2;;
fsl-5.0.8/src/feat5/fsl_motion_outliers-151- -o)
fsl-5.0.8/src/feat5/fsl_motion_outliers:152: outfile=`get_arg2 $1 $2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-153- shift 2;;
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-155- do_make_mask=no;
fsl-5.0.8/src/feat5/fsl_motion_outliers:156: mask=`get_arg2 $1 $2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-157- shift 2;;
fsl-5.0.8/src/feat5/fsl_motion_outliers-158- -s)
fsl-5.0.8/src/feat5/fsl_motion_outliers:159: savefile=`get_arg2 $1 $2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-160- shift 2;;
fsl-5.0.8/src/feat5/fsl_motion_outliers-161- -p)
fsl-5.0.8/src/feat5/fsl_motion_outliers:162: plotfile=`get_arg2 $1 $2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-163- shift 2;;
fsl-5.0.8/src/feat5/fsl_motion_outliers-164- -t)
fsl-5.0.8/src/feat5/fsl_motion_outliers:165: tmppath=`get_arg2 $1 $2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-166- shift 2;;
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-189- --dummy)
fsl-5.0.8/src/feat5/fsl_motion_outliers:190: ndel=`get_arg1 $1`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-191- shift;;
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-193- use_abs_thresh=yes;
fsl-5.0.8/src/feat5/fsl_motion_outliers:194: abs_thresh=`get_arg1 $1`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-195- shift;;
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-202- *)
fsl-5.0.8/src/feat5/fsl_motion_outliers:203: if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then
fsl-5.0.8/src/feat5/fsl_motion_outliers-204- if [ $niter = 1 -a $# -eq 3 ] ; then
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-222-#### PARSE OPTIONS
fsl-5.0.8/src/feat5/fsl_motion_outliers:223:mcf=`$FSLDIR/bin/remove_ext $mcf`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:224:outfile=`$FSLDIR/bin/remove_ext $outfile`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-225-if [ X$ndel = X ] ; then ndel=0; fi
fsl-5.0.8/src/feat5/fsl_motion_outliers:226:if [ $do_make_mask = no ] ; then mask=`$FSLDIR/bin/remove_ext $mask`; fi
fsl-5.0.8/src/feat5/fsl_motion_outliers-227-if [ $verbose = yes ] ; then echo "mcf = $mcf ; outfile = $outfile ; ndel = $ndel ; mask = $mask ; do_moco = $do_moco ; thresh = $abs_thresh ; use_thresh = $use_abs_thresh ; metric = $metric"; fi
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-237-# output dir creation
fsl-5.0.8/src/feat5/fsl_motion_outliers:238:outdir=`$FSLDIR/bin/tmpnam`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-239-
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-241-if [ X${tmppath} != X ] ; then
fsl-5.0.8/src/feat5/fsl_motion_outliers:242: outdir=${tmppath}/`basename ${outdir}`
fsl-5.0.8/src/feat5/fsl_motion_outliers-243-fi
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-252-#### DELETE DUMMY SCANS
fsl-5.0.8/src/feat5/fsl_motion_outliers:253:nvol=`$FSLDIR/bin/fslval $mcf dim4`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:254:nvol=`echo $nvol - $ndel | bc`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-255-if [ $ndel -gt 0 ] ; then
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-261-#### MOTION CORRECTION
fsl-5.0.8/src/feat5/fsl_motion_outliers:262:refnum=`$FSLDIR/bin/fslval $mcf dim4`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:263:refnum=`echo $refnum / 2 | bc`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-264-if [ $do_moco = yes ] ; then
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-271-
fsl-5.0.8/src/feat5/fsl_motion_outliers:272:tmax=`$FSLDIR/bin/fslval ${mcf} dim4`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:273:tmax1=`echo $tmax - 1 | bc`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-274-
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-278- mask=${outdir}_mc/mask
fsl-5.0.8/src/feat5/fsl_motion_outliers:279: thr2=`$FSLDIR/bin/fslstats $mcf -P 2`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:280: thr98=`$FSLDIR/bin/fslstats $mcf -P 98`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:281: robthr=`echo "$thr2 + 0.1 * ( $thr98 - $thr2 )" | bc -l`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-282- $FSLDIR/bin/fslmaths $mcf -Tmean -thr $robthr -bin $mask
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-287-# normalise by percentage of mask voxels and by median value within the brain
fsl-5.0.8/src/feat5/fsl_motion_outliers:288:brainmed=`$FSLDIR/bin/fslstats ${mcf} -k ${mask} -P 50`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:289:maskmean=`$FSLDIR/bin/fslstats ${mask} -m`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-290-if [ $verbose = yes ] ; then echo "brainmed = $brainmed ; maskmean = $maskmean" ; fi
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-367- # calculate box-plot outlier limits
fsl-5.0.8/src/feat5/fsl_motion_outliers:368: pv=`$FSLDIR/bin/fslstats ${outdir}_mc/res_mse_diff -p 25 -p 75`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:369: p25=`echo $pv | awk '{ print $1 }'`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:370: p75=`echo $pv | awk '{ print $2 }'`;
fsl-5.0.8/src/feat5/fsl_motion_outliers:371: threshv=`echo "$p75 + 1.5 * ( $p75 - $p25 )" | bc -l`
fsl-5.0.8/src/feat5/fsl_motion_outliers-372-fi
fsl-5.0.8/src/feat5/fsl_motion_outliers:373:if [ $verbose = yes ] ; then echo "Range of metric values: `$FSLDIR/bin/fslstats ${outdir}_mc/res_mse_diff -R`" ; fi
fsl-5.0.8/src/feat5/fsl_motion_outliers-374-
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-383-$FSLDIR/bin/fslmerge -t ${outdir}_mc/outliers ${outdir}_mc/zero ${outdir}_mc/outliers
fsl-5.0.8/src/feat5/fsl_motion_outliers:384:nmax=`$FSLDIR/bin/fslstats ${outdir}_mc/outliers -V | awk '{ print $1 }'`
fsl-5.0.8/src/feat5/fsl_motion_outliers-385-if [ $verbose = yes ] ; then echo "Found $nmax outliers over $threshv"; fi
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-395- $FSLDIR/bin/fslmaths ${outdir}_mc/outliers -roi 0 1 0 1 0 1 $n 1 ${outdir}_mc/stp
fsl-5.0.8/src/feat5/fsl_motion_outliers:396: val=`$FSLDIR/bin/fslstats ${outdir}_mc/stp -V | awk '{ print $1 }'`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-397- if [ $val -gt 0 ] ; then
##############################################
fsl-5.0.8/src/feat5/fsl_motion_outliers-407- fi
fsl-5.0.8/src/feat5/fsl_motion_outliers:408: n=`echo "$n + 1" | bc`;
fsl-5.0.8/src/feat5/fsl_motion_outliers-409-done
##############################################
fsl-5.0.8/src/feat5/mp_diffpow.sh-80-
fsl-5.0.8/src/feat5/mp_diffpow.sh:81:f=`echo $2 | sed 's/\....$//'`
fsl-5.0.8/src/feat5/mp_diffpow.sh-82-
##############################################
fsl-5.0.8/src/feat5/pnm.tcl-359- puts $pnms3 "$pnmcommand"
fsl-5.0.8/src/feat5/pnm.tcl:360: puts $pnms3 "ls -1 `$FSLDIR/bin/imglob -extensions \$\{obase\}ev0*` > ${outname}_evlist.txt"
fsl-5.0.8/src/feat5/pnm.tcl-361- close $pnms3
##############################################
fsl-5.0.8/src/feat5/checkFEAT-67-Usage() {
fsl-5.0.8/src/feat5/checkFEAT:68: function=`basename $0`
fsl-5.0.8/src/feat5/checkFEAT-69- echo Usage: $function FEATdirs
##############################################
fsl-5.0.8/src/feat5/checkFEAT-79-
fsl-5.0.8/src/feat5/checkFEAT:80: do a=`grep -o 'STILL RUNNING' $aa/report.html`
fsl-5.0.8/src/feat5/checkFEAT:81: b=`grep -o 'Errors occured' $aa/report.html`
fsl-5.0.8/src/feat5/checkFEAT:82: bb=`grep -l 'Error' $aa/report_log.html`
fsl-5.0.8/src/feat5/checkFEAT-83-
##############################################
fsl-5.0.8/src/feat5/autoaq-63-# Prepare a random string to save temporary files
fsl-5.0.8/src/feat5/autoaq:64:TMPNAME=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/feat5/autoaq-65-
##############################################
fsl-5.0.8/src/feat5/updatefeatreg-72-usage() {
fsl-5.0.8/src/feat5/updatefeatreg:73: echo "Usage: `basename $0` <feat_directory> [-pngs]"
fsl-5.0.8/src/feat5/updatefeatreg-74- echo " Updates all inverse and concatenated transforms in a first-level"
##############################################
fsl-5.0.8/src/feat5/updatefeatreg-89- if [ -f ${1}.mat ] ; then
fsl-5.0.8/src/feat5/updatefeatreg:90: a=`echo $1 | awk -F 2 '{print $1}'`
fsl-5.0.8/src/feat5/updatefeatreg:91: b=`echo $1 | awk -F 2 '{print $2}'`
fsl-5.0.8/src/feat5/updatefeatreg-92- echo inverting ${1}.mat
##############################################
fsl-5.0.8/src/feat5/updatefeatreg-97-picupdate() {
fsl-5.0.8/src/feat5/updatefeatreg:98: if [ `${FSLDIR}/bin/imtest $1` = 1 ] && [ `${FSLDIR}/bin/imtest $2` = 1 ] && [ -f ${1}2${2}.mat ] ; then
fsl-5.0.8/src/feat5/updatefeatreg-99- out=${1}2${2}
fsl-5.0.8/src/feat5/updatefeatreg-100- echo creating summary picture for ${out}
fsl-5.0.8/src/feat5/updatefeatreg:101: if [ $1 = "example_func" ] && [ $2 = "standard" ] && [ `${FSLDIR}/bin/imtest highres2standard_warp` = 1 ] ; then
fsl-5.0.8/src/feat5/updatefeatreg-102- ${FSLDIR}/bin/applywarp --ref=$2 --in=$1 --out=$out --warp=highres2standard_warp --premat=${1}2highres.mat
fsl-5.0.8/src/feat5/updatefeatreg:103: elif [ $1 = "highres" ] && [ $2 = "standard" ] && [ `${FSLDIR}/bin/imtest highres2standard_warp` = 1 ] ; then
fsl-5.0.8/src/feat5/updatefeatreg-104- ${FSLDIR}/bin/applywarp --ref=$2 --in=$1 --out=$out --warp=highres2standard_warp
##############################################
fsl-5.0.8/src/feat5/invfeatreg-80-
fsl-5.0.8/src/feat5/invfeatreg:81:if [ `${FSLDIR}/bin/imtest highres2standard_warp` -a `${FSLDIR}/bin/imtest highres2standard_warp_inv` = 0 ] ; then
fsl-5.0.8/src/feat5/invfeatreg-82- echo "Found nonlinear warp field...starting warp field inversion..."
##############################################
fsl-5.0.8/src/feat5/easythresh-84- [ "$4" = "" ] && Usage
fsl-5.0.8/src/feat5/easythresh:85: MAX=`${FSLDIR}/bin/fslstats $1 -R | awk '{print $2}'`
fsl-5.0.8/src/feat5/easythresh-86- ${FSLDIR}/bin/overlay 1 0 $3 -a $1 $2 $MAX rendered_$4
##############################################
fsl-5.0.8/src/feat5/easythresh-93-# estimate image smoothness
fsl-5.0.8/src/feat5/easythresh:94:SM=`${FSLDIR}/bin/smoothest -z $1 -m $2`
fsl-5.0.8/src/feat5/easythresh:95:DLH=`echo $SM | awk '{print $2}'`
fsl-5.0.8/src/feat5/easythresh:96:VOLUME=`echo $SM | awk '{print $4}'`
fsl-5.0.8/src/feat5/easythresh:97:RESELS=`echo $SM | awk '{print $6}'`
fsl-5.0.8/src/feat5/easythresh-98-#echo "$DLH $VOLUME $RESELS"
##############################################
fsl-5.0.8/src/feat5/easythresh-105-# colour rendering
fsl-5.0.8/src/feat5/easythresh:106:MAX=`${FSLDIR}/bin/fslstats thresh_$6 -R | awk '{print $2}'`
fsl-5.0.8/src/feat5/easythresh-107-${FSLDIR}/bin/overlay 1 0 $5 -a thresh_$6 $3 $MAX rendered_thresh_$6
##############################################
fsl-5.0.8/src/feat5/perfusion_subtract-80-[ "$2" = "" ] && Usage
fsl-5.0.8/src/feat5/perfusion_subtract:81:IN=`$FSLDIR/bin/remove_ext $1`
fsl-5.0.8/src/feat5/perfusion_subtract:82:OUT=`$FSLDIR/bin/remove_ext $2`
fsl-5.0.8/src/feat5/perfusion_subtract-83-shift 2
fsl-5.0.8/src/feat5/perfusion_subtract-84-
fsl-5.0.8/src/feat5/perfusion_subtract:85:tmpbase=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/feat5/perfusion_subtract-86-invert=""
##############################################
fsl-5.0.8/src/feat5/perfusion_subtract-107-
fsl-5.0.8/src/feat5/perfusion_subtract:108:${FSLDIR}/bin/fslmerge -t even `${FSLDIR}/bin/imglob vol*[02468].*`
fsl-5.0.8/src/feat5/perfusion_subtract:109:${FSLDIR}/bin/fslmerge -t odd `${FSLDIR}/bin/imglob vol*[13579].*`
fsl-5.0.8/src/feat5/perfusion_subtract-110-
fsl-5.0.8/src/feat5/perfusion_subtract:111:if [ `${FSLDIR}/bin/fslnvols even` != `${FSLDIR}/bin/fslnvols odd` ] ; then
fsl-5.0.8/src/feat5/perfusion_subtract-112- echo "Warning - odd number of timepoints in input data - will ignore last timepoint"
fsl-5.0.8/src/feat5/perfusion_subtract:113: ${FSLDIR}/bin/fslroi even even 0 `${FSLDIR}/bin/fslnvols odd`
fsl-5.0.8/src/feat5/perfusion_subtract-114-fi
##############################################
fsl-5.0.8/src/feat5/perfusion_subtract-124-
fsl-5.0.8/src/feat5/perfusion_subtract:125:la=`${FSLDIR}/bin/imglob -extension [eo]_*`
fsl-5.0.8/src/feat5/perfusion_subtract:126:lb=`ls -1 $la | sort -t _ -k 2`
fsl-5.0.8/src/feat5/perfusion_subtract-127-${FSLDIR}/bin/fslmerge -t output $lb
##############################################
fsl-5.0.8/src/fslsurface/first_utils.sh-108- elif [ $1 = "--useRigidAlign" ] ; then
fsl-5.0.8/src/fslsurface/first_utils.sh:109: DOF=`echo "${DOF}+6" | bc`
fsl-5.0.8/src/fslsurface/first_utils.sh-110- shift 1
fsl-5.0.8/src/fslsurface/first_utils.sh-111- elif [ $1 = "--useScale" ] ; then
fsl-5.0.8/src/fslsurface/first_utils.sh:112: DOF=`echo "${DOF}+1" | bc`
fsl-5.0.8/src/fslsurface/first_utils.sh-113- shift 1
##############################################
fsl-5.0.8/src/fslsurface/first_utils.sh-152- fi
fsl-5.0.8/src/fslsurface/first_utils.sh:153: for surf in `cat ${outname}_list.txt` ; do
fsl-5.0.8/src/fslsurface/first_utils.sh-154- echo "Registering surface ${surf}..."
fsl-5.0.8/src/fslsurface/first_utils.sh-155-# echo ${fsurf}_2_mni_dof${DOF}.gii
fsl-5.0.8/src/fslsurface/first_utils.sh:156: fsurf=`basename $surf .gii`
fsl-5.0.8/src/fslsurface/first_utils.sh:157: fsurf=`basename $surf .vtk`
fsl-5.0.8/src/fslsurface/first_utils.sh:158: dsurf=`dirname $surf`
fsl-5.0.8/src/fslsurface/first_utils.sh-159- # echo ${fsurf}_to_mni_dof${DOF}.gii
##############################################
fsl-5.0.8/src/fslsurface/first_utils.sh-162- #./build/Debug/fslsurface_utils --doLeastSquaresReg -s $surf -r ${outname}_mean_mni.gii -o ${fsurf}_2_mni_dof${DOF}.gii -d ${DOF}
fsl-5.0.8/src/fslsurface/first_utils.sh:163: fsurf=`basename $surf .gii`
fsl-5.0.8/src/fslsurface/first_utils.sh-164- ${FSLDIR}/bin/fslsurfacemaths $surf -reg_lq ${reffile} ${DOF} ${dsurf}/${fsurf}_to_mni_dof${DOF}.mat ${dsurf}/${fsurf}_to_mni_dof${DOF}.gii
##############################################
fsl-5.0.8/src/fslsurface/first_utils.sh-188- if [ $useBvars = 1 ] ; then
fsl-5.0.8/src/fslsurface/first_utils.sh:189: rm `cat ${outname}_surfaces_aligned.txt` `cat ${outname}_list.txt`
fsl-5.0.8/src/fslsurface/first_utils.sh-190- fi
##############################################
fsl-5.0.8/src/cluster/cluster2html-93-
fsl-5.0.8/src/cluster/cluster2html:94: lmaxname=`echo $1 | sed "s/cluster/lmax/g"`.txt
fsl-5.0.8/src/cluster/cluster2html-95- if [ -f $lmaxname ] ; then
##############################################
fsl-5.0.8/src/cluster/cluster2html-119-
fsl-5.0.8/src/cluster/cluster2html:120: lmaxname=`echo $1 | sed "s/cluster/lmax/g"`_std.txt
fsl-5.0.8/src/cluster/cluster2html-121- if [ -f $lmaxname ] ; then
##############################################
fsl-5.0.8/src/tbss/tbss_non_FA-91-fi
fsl-5.0.8/src/tbss/tbss_non_FA:92:for f in `$FSLDIR/bin/imglob *_FA.*` ; do
fsl-5.0.8/src/tbss/tbss_non_FA:93: f=` echo $f | sed 's/_FA$//g'`
fsl-5.0.8/src/tbss/tbss_non_FA-94- echo $f
##############################################
fsl-5.0.8/src/tbss/tbss_non_FA-98-echo "merging all upsampled $ALTIM images into single 4D image"
fsl-5.0.8/src/tbss/tbss_non_FA:99:${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.*`
fsl-5.0.8/src/tbss/tbss_non_FA-100-cd ../stats
##############################################
fsl-5.0.8/src/tbss/tbss_fill-87- # renorm so that the max is same as input's max
fsl-5.0.8/src/tbss/tbss_fill:88: $FSLDIR/bin/fslmaths $OUT -div `${FSLDIR}/bin/fslstats $OUT -p 100` -mul `${FSLDIR}/bin/fslstats $IN -p 100` $OUT
fsl-5.0.8/src/tbss/tbss_fill-89-
##############################################
fsl-5.0.8/src/tbss/tbss_fill-91- # then multiply by mean-FA (to ensure we stay within real tracts)
fsl-5.0.8/src/tbss/tbss_fill:92: $FSLDIR/bin/fslmaths $IN -thr $THRESH -add $OUT -div 2 -mul $MEANFA -div `${FSLDIR}/bin/fslstats $MEANFA -p 100` $OUT -odt float
fsl-5.0.8/src/tbss/tbss_fill-93-
fsl-5.0.8/src/tbss/tbss_fill-94- # final thresholding at 1/50 of max value
fsl-5.0.8/src/tbss/tbss_fill:95: $FSLDIR/bin/fslmaths $OUT -thr `${FSLDIR}/bin/fslstats $OUT -R | awk '{print "10 k " $2 " 50 / p"}' | dc -` $OUT
fsl-5.0.8/src/tbss/tbss_fill-96-}
##############################################
fsl-5.0.8/src/tbss/tbss_fill-104-
fsl-5.0.8/src/tbss/tbss_fill:105:if [ `${FSLDIR}/bin/imtest $STATS` = 0 ] || [ `${FSLDIR}/bin/imtest $MEANFA` = 0 ] ; then
fsl-5.0.8/src/tbss/tbss_fill-106- echo "Error - either <stats_image> or <mean_FA> is not valid"
##############################################
fsl-5.0.8/src/tbss/tbss_2_reg-89-
fsl-5.0.8/src/tbss/tbss_2_reg:90: for g in `$FSLDIR/bin/imglob *_FA.*` ; do
fsl-5.0.8/src/tbss/tbss_2_reg-91-
##############################################
fsl-5.0.8/src/tbss/tbss_2_reg-110- cd FA
fsl-5.0.8/src/tbss/tbss_2_reg:111: for f in `$FSLDIR/bin/imglob *_FA.*` ; do
fsl-5.0.8/src/tbss/tbss_2_reg-112- do_reg $f
##############################################
fsl-5.0.8/src/tbss/tbss_2_reg-121- fi
fsl-5.0.8/src/tbss/tbss_2_reg:122: if [ `${FSLDIR}/bin/imtest $TARGET` = 0 ] ; then
fsl-5.0.8/src/tbss/tbss_2_reg-123- echo ""
##############################################
fsl-5.0.8/src/tbss/fsl_reg-87-[ "$3" = "" ] && Usage
fsl-5.0.8/src/tbss/fsl_reg:88:INPUT=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/tbss/fsl_reg:89:REFERENCE=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/tbss/fsl_reg-90-I2R=$3
##############################################
fsl-5.0.8/src/tbss/fsl_reg-121-# do the registration
fsl-5.0.8/src/tbss/fsl_reg:122:if [ `${FSLDIR}/bin/imtest ${INPUT}_mask` = 1 ] ; then
fsl-5.0.8/src/tbss/fsl_reg-123- INMASK="-inweight ${INPUT}_mask"
##############################################
fsl-5.0.8/src/tbss/tbss_1_preproc-85-
fsl-5.0.8/src/tbss/tbss_1_preproc:86:for f in `$FSLDIR/bin/imglob $@` ; do
fsl-5.0.8/src/tbss/tbss_1_preproc-87-
##############################################
fsl-5.0.8/src/tbss/tbss_1_preproc-90- # erode a little and zero end slices
fsl-5.0.8/src/tbss/tbss_1_preproc:91: X=`${FSLDIR}/bin/fslval $f dim1`; X=`echo "$X 2 - p" | dc -`
fsl-5.0.8/src/tbss/tbss_1_preproc:92: Y=`${FSLDIR}/bin/fslval $f dim2`; Y=`echo "$Y 2 - p" | dc -`
fsl-5.0.8/src/tbss/tbss_1_preproc:93: Z=`${FSLDIR}/bin/fslval $f dim3`; Z=`echo "$Z 2 - p" | dc -`
fsl-5.0.8/src/tbss/tbss_1_preproc-94- $FSLDIR/bin/fslmaths $f -min 1 -ero -roi 1 $X 1 $Y 1 $Z 0 1 FA/${f}_FA
##############################################
fsl-5.0.8/src/tbss/tbss_1_preproc-106-cd FA
fsl-5.0.8/src/tbss/tbss_1_preproc:107:$FSLDIR/bin/slicesdir `$FSLDIR/bin/imglob *_FA.*` > grot 2>&1
fsl-5.0.8/src/tbss/tbss_1_preproc-108-cat grot | tail -n 2
##############################################
fsl-5.0.8/src/tbss/tbss_sym-85-
fsl-5.0.8/src/tbss/tbss_sym:86:if [ `${FSLDIR}/bin/imtest mean_FA_symmetrised_skeleton_mask_dst` -eq 0 ]; then
fsl-5.0.8/src/tbss/tbss_sym-87-
##############################################
fsl-5.0.8/src/tbss/tbss_sym-111-$FSLDIR/bin/fslswapdim all_${ALTIM}_symmetrised_skeletonised -x y z grotsym_all_${ALTIM}_symmetrised_flipped > /dev/null
fsl-5.0.8/src/tbss/tbss_sym:112:$FSLDIR/bin/fslmaths all_${ALTIM}_symmetrised_skeletonised -sub grotsym_all_${ALTIM}_symmetrised_flipped -roi 91 91 0 218 0 182 0 `$FSLDIR/bin/fslval all_FA_skeletonised dim4` all_${ALTIM}_skeletonised_left_minus_right
fsl-5.0.8/src/tbss/tbss_sym-113-
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-100-
fsl-5.0.8/src/tbss/tbss_3_postreg:101:if [ `${FSLDIR}/bin/imtest target` = 1 ] ; then
fsl-5.0.8/src/tbss/tbss_3_postreg-102- echo "using pre-chosen target for registration"
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-106-
fsl-5.0.8/src/tbss/tbss_3_postreg:107: n=`$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr* | wc -w`
fsl-5.0.8/src/tbss/tbss_3_postreg-108-
fsl-5.0.8/src/tbss/tbss_3_postreg:109: for f in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do
fsl-5.0.8/src/tbss/tbss_3_postreg-110-
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-113-
fsl-5.0.8/src/tbss/tbss_3_postreg:114: for g in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do
fsl-5.0.8/src/tbss/tbss_3_postreg-115-
fsl-5.0.8/src/tbss/tbss_3_postreg:116: thismeanscore=`cat ${g}_to_${f}_warp.msf | awk '{print $1}'`
fsl-5.0.8/src/tbss/tbss_3_postreg:117: thismedianscore=`cat ${g}_to_${f}_warp.msf | awk '{print $2}'`
fsl-5.0.8/src/tbss/tbss_3_postreg-118-
fsl-5.0.8/src/tbss/tbss_3_postreg:119: meanscore=`echo "10 k $meanscore $thismeanscore + p" | dc -`
fsl-5.0.8/src/tbss/tbss_3_postreg:120: medianscore=`echo "10 k $medianscore $thismedianscore + p" | dc -`
fsl-5.0.8/src/tbss/tbss_3_postreg-121- done
fsl-5.0.8/src/tbss/tbss_3_postreg-122-
fsl-5.0.8/src/tbss/tbss_3_postreg:123: meanscore=`echo "10 k $meanscore $n / p" | dc -`
fsl-5.0.8/src/tbss/tbss_3_postreg:124: medianscore=`echo "10 k $medianscore $n / p" | dc -`
fsl-5.0.8/src/tbss/tbss_3_postreg-125-
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-130-
fsl-5.0.8/src/tbss/tbss_3_postreg:131: best=`cat all.msf | sort -k 2 -n | head -n 1 | awk '{print $1}'`
fsl-5.0.8/src/tbss/tbss_3_postreg-132- echo "best target is $best - now registering this to standard space"
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-141-# is target already in MNI152 space? (kludge)
fsl-5.0.8/src/tbss/tbss_3_postreg:142:if [ `${FSLDIR}/bin/imtest target` = 1 ] && [ `$FSLDIR/bin/fslval $best dim1` = 182 ] && [ `$FSLDIR/bin/fslval $best dim2` = 218 ] && [ `$FSLDIR/bin/fslval $best dim3` = 182 ] ; then
fsl-5.0.8/src/tbss/tbss_3_postreg-143-
fsl-5.0.8/src/tbss/tbss_3_postreg-144- echo "transforming all FA images into MNI152 space"
fsl-5.0.8/src/tbss/tbss_3_postreg:145: filelist=`$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*`;
fsl-5.0.8/src/tbss/tbss_3_postreg-146- # check that all the registration results are there!
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-148- for f in $filelist ; do
fsl-5.0.8/src/tbss/tbss_3_postreg:149: if [ `${FSLDIR}/bin/imtest ${f}_to_target_warp` = 0 ] ; then
fsl-5.0.8/src/tbss/tbss_3_postreg-150- missingwarps="$missingwarps ${f}_to_target_warp"
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-152- done
fsl-5.0.8/src/tbss/tbss_3_postreg:153: if [ `echo $missingwarps | wc -c` -gt 1 ] ; then
fsl-5.0.8/src/tbss/tbss_3_postreg-154- echo "ERROR:: cannot find the following warp results:"
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-170- echo "transforming (and upsampling) all FA images into MNI152 space"
fsl-5.0.8/src/tbss/tbss_3_postreg:171: for f in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do
fsl-5.0.8/src/tbss/tbss_3_postreg-172- echo $f
##############################################
fsl-5.0.8/src/tbss/tbss_3_postreg-178-echo "merging all upsampled FA images into single 4D image"
fsl-5.0.8/src/tbss/tbss_3_postreg:179:${FSLDIR}/bin/fslmerge -t ../stats/all_FA `$FSLDIR/bin/imglob *_FA_to_target.*`
fsl-5.0.8/src/tbss/tbss_3_postreg-180-cd ../stats
##############################################
fsl-5.0.8/src/tbss/tbss_deproject-85-[ "$2" = "" ] && Usage
fsl-5.0.8/src/tbss/tbss_deproject:86:IN=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/tbss/tbss_deproject-87-SPACE=$2
##############################################
fsl-5.0.8/src/tbss/tbss_deproject-112- cd ../FA
fsl-5.0.8/src/tbss/tbss_deproject:113: list=`$FSLDIR/bin/imglob *_FA.*`
fsl-5.0.8/src/tbss/tbss_deproject-114- echo list of original images = $list
##############################################
fsl-5.0.8/src/tbss/tbss_deproject-119- echo "processing ${g}:"
fsl-5.0.8/src/tbss/tbss_deproject:120: nextvol=`$FSLDIR/bin/imglob ../stats/${IN}_to_all_FA_tmp0* | awk '{print $1}'`
fsl-5.0.8/src/tbss/tbss_deproject-121- warp=${g}_to_${target}_warp
fsl-5.0.8/src/tbss/tbss_deproject:122: if [ `$FSLDIR/bin/imtest ${warp}_inv` = 0 ] ; then
fsl-5.0.8/src/tbss/tbss_deproject-123- $FSLDIR/bin/invwarp -w $warp -o ${warp}_inv -r $g
##############################################
fsl-5.0.8/src/tbss/tbss_deproject-127-
fsl-5.0.8/src/tbss/tbss_deproject:128: maxn=`${FSLDIR}/bin/fslstats $nextvol -R | awk '{print "0 k " $2 " 0.5 + 1 / p" }' | dc - `
fsl-5.0.8/src/tbss/tbss_deproject-129- echo "max label value = $maxn"
##############################################
fsl-5.0.8/src/tbss/tbss_deproject-132- echo processing label $i
fsl-5.0.8/src/tbss/tbss_deproject:133: nextout=${nextvol}_split_`${FSLDIR}/bin/zeropad $i 5`
fsl-5.0.8/src/tbss/tbss_deproject-134- ${FSLDIR}/bin/fslmaths $nextvol -thr $i -uthr $i -bin $nextout
fsl-5.0.8/src/tbss/tbss_deproject-135- ${FSLDIR}/bin/applywarp -i $nextout -o $nextout -r $g -w ${warp}_inv --rel $preaffine -d float -s --superlevel=a
fsl-5.0.8/src/tbss/tbss_deproject:136: i=`echo "$i 1 + p" | dc -`
fsl-5.0.8/src/tbss/tbss_deproject-137- done
fsl-5.0.8/src/tbss/tbss_deproject-138- echo "combining across label values"
fsl-5.0.8/src/tbss/tbss_deproject:139: ${FSLDIR}/bin/fslmerge -t ${g}_${IN} `${FSLDIR}/bin/imglob ${nextvol}_split_*`
fsl-5.0.8/src/tbss/tbss_deproject-140- ${FSLDIR}/bin/fslmaths ${g}_${IN} -thr 0.1 -Tmax -bin $nextvol
##############################################
fsl-5.0.8/src/tbss/tbss_x-84-for d in $@ ; do
fsl-5.0.8/src/tbss/tbss_x:85: cnt=`echo "$cnt+1" | bc -l`
fsl-5.0.8/src/tbss/tbss_x-86-done
##############################################
fsl-5.0.8/src/tbss/tbss_x-114- echo $m
fsl-5.0.8/src/tbss/tbss_x:115: for f in `$FSLDIR/bin/imglob *` ; do
fsl-5.0.8/src/tbss/tbss_x:116: ff=`$FSLDIR/bin/remove_ext $f`
fsl-5.0.8/src/tbss/tbss_x-117- echo $ff
##############################################
fsl-5.0.8/src/tbss/tbss_x-132- echo $m
fsl-5.0.8/src/tbss/tbss_x:133: for f in `$FSLDIR/bin/imglob *` ; do
fsl-5.0.8/src/tbss/tbss_x:134: ff=`$FSLDIR/bin/remove_ext $f`
fsl-5.0.8/src/tbss/tbss_x-135- echo $ff
##############################################
fsl-5.0.8/src/tbss/tbss_x-155- echo $m
fsl-5.0.8/src/tbss/tbss_x:156: $FSLDIR/bin/fslmerge -t ../stats/all_${m} `$FSLDIR/bin/imglob *_to_target_${m}.*`
fsl-5.0.8/src/tbss/tbss_x-157- $FSLDIR/bin/fslmaths ../stats/all_${m} -mas ../stats/mean_FA_mask ../stats/all_${m}
##############################################
fsl-5.0.8/src/tbss/tbss_x-162- for xyz in x y z;do
fsl-5.0.8/src/tbss/tbss_x:163: for f in `$FSLDIR/bin/imglob *_to_target_${m}.*` ; do
fsl-5.0.8/src/tbss/tbss_x-164- echo $f
fsl-5.0.8/src/tbss/tbss_x:165: fslroi ${f} `$FSLDIR/bin/remove_ext ${f}`_${xyz} ${i} 1
fsl-5.0.8/src/tbss/tbss_x-166- done
fsl-5.0.8/src/tbss/tbss_x:167: $FSLDIR/bin/fslmerge -t ../stats/all_${m}_${xyz} `$FSLDIR/bin/imglob *_to_target_${m}_${xyz}.*`
fsl-5.0.8/src/tbss/tbss_x-168- $FSLDIR/bin/fslmaths ../stats/all_${m}_${xyz} -mas ../stats/mean_FA_mask ../stats/all_${m}_${xyz}
fsl-5.0.8/src/tbss/tbss_x:169: $FSLDIR/bin/imrm `$FSLDIR/bin/imglob *_to_target_${m}_${xyz}.*`
fsl-5.0.8/src/tbss/tbss_x-170- let "i+=1"
##############################################
fsl-5.0.8/src/tbss/tbss_x-203- $FSLDIR/bin/fslsplit all_${m}_skeletonised all_${m}_skeletonised_
fsl-5.0.8/src/tbss/tbss_x:204: for im in `$FSLDIR/bin/imglob all_${m}_skeletonised_????.*` ; do
fsl-5.0.8/src/tbss/tbss_x:205: n=`echo $im | sed s/all_"${m}"_skeletonised_//g`
fsl-5.0.8/src/tbss/tbss_x-206- echo $im >> .scalist${n}.txt
##############################################
fsl-5.0.8/src/tbss/tbss_x-214- done
fsl-5.0.8/src/tbss/tbss_x:215: for im in `$FSLDIR/bin/imglob all_${m}_x_skeletonised_????.*` ; do
fsl-5.0.8/src/tbss/tbss_x:216: n=`echo $im | sed s/all_"${m}"_x_skeletonised_//g`
fsl-5.0.8/src/tbss/tbss_x-217- $FSLDIR/bin/fslmerge -t all_${m}_skeletonised_$n all_${m}_x_skeletonised_$n all_${m}_y_skeletonised_$n all_${m}_z_skeletonised_$n
##############################################
fsl-5.0.8/src/tbss/tbss_x-228-for list in .scalist????.txt ; do
fsl-5.0.8/src/tbss/tbss_x:229: n=`echo $list | sed s/.scalist//g | sed s/.txt//g`
fsl-5.0.8/src/tbss/tbss_x-230- subjscalist=.scalist${n}.txt
##############################################
fsl-5.0.8/src/tbss/tbss_x-233- fslmaths mean_FA_skeleton_mask mfibresmask
fsl-5.0.8/src/tbss/tbss_x:234: for f in `cat $subjscalist` ; do
fsl-5.0.8/src/tbss/tbss_x-235- fslmaths $f -thr .1 -bin -mas mfibresmask mfibresmask
##############################################
fsl-5.0.8/src/tbss/tbss_x-257-for i in .scalist????.txt ; do
fsl-5.0.8/src/tbss/tbss_x:258: n=`echo $i | sed s/.scalist//g | sed s/.txt//g`
fsl-5.0.8/src/tbss/tbss_x-259- mm=1
##############################################
fsl-5.0.8/src/fugue/invwarp-107- aa=$1;
fsl-5.0.8/src/fugue/invwarp:108: bb=`echo $aa | sed 's/=.*//'`;
fsl-5.0.8/src/fugue/invwarp:109: cc=`echo $aa | sed 's/.*=//'`;
fsl-5.0.8/src/fugue/invwarp-110- if [ $aa = "-w" ] ; then
##############################################
fsl-5.0.8/src/fugue/invwarp-154-fi
fsl-5.0.8/src/fugue/invwarp:155:if [ `$FSLDIR/bin/imtest $refvol` = 0 ] ; then Usage ; fi
fsl-5.0.8/src/fugue/invwarp:156:if [ `$FSLDIR/bin/imtest $inwarp` = 0 ] ; then Usage ; fi
fsl-5.0.8/src/fugue/invwarp-157-if [ X$outvol = X ] ; then Usage ; fi
##############################################
fsl-5.0.8/src/fugue/invwarp-160-if [ $verbose = yes ] ; then echo "Extracting ROI" ; fi
fsl-5.0.8/src/fugue/invwarp:161:roivals=`$FSLDIR/bin/fslstats $refvol -w`;
fsl-5.0.8/src/fugue/invwarp-162-
fsl-5.0.8/src/fugue/invwarp:163:xmin=`echo $roivals | awk '{ print $1 }'`;
fsl-5.0.8/src/fugue/invwarp:164:ymin=`echo $roivals | awk '{ print $3 }'`;
fsl-5.0.8/src/fugue/invwarp:165:zmin=`echo $roivals | awk '{ print $5 }'`;
fsl-5.0.8/src/fugue/invwarp:166:xsize=`echo $roivals | awk '{ print $2 }'`;
fsl-5.0.8/src/fugue/invwarp:167:ysize=`echo $roivals | awk '{ print $4 }'`;
fsl-5.0.8/src/fugue/invwarp:168:zsize=`echo $roivals | awk '{ print $6 }'`;
fsl-5.0.8/src/fugue/invwarp-169-
##############################################
fsl-5.0.8/src/fugue/invwarp-177- if [ $zsize -gt 180 ] ; then badroi=yes; fi
fsl-5.0.8/src/fugue/invwarp:178: if [ `$FSLDIR/bin/fslval $refvol dim1` -le `echo "$xsize + 2" | bc` ] ; then
fsl-5.0.8/src/fugue/invwarp:179: if [ `$FSLDIR/bin/fslval $refvol dim2` -le `echo "$ysize + 2" | bc` ] ; then
fsl-5.0.8/src/fugue/invwarp:180: if [ `$FSLDIR/bin/fslval $refvol dim3` -le `echo "$zsize + 2" | bc` ] ; then
fsl-5.0.8/src/fugue/invwarp-181- badroi=yes;
##############################################
fsl-5.0.8/src/fugue/invwarp-195-if [ $xmin -ge 2 ] ; then
fsl-5.0.8/src/fugue/invwarp:196: xmin=`echo $xmin - 2 | bc`;
fsl-5.0.8/src/fugue/invwarp:197: xsize=`echo $xsize + 2 | bc`;
fsl-5.0.8/src/fugue/invwarp-198-fi
fsl-5.0.8/src/fugue/invwarp-199-if [ $ymin -ge 2 ] ; then
fsl-5.0.8/src/fugue/invwarp:200: ymin=`echo $ymin - 2 | bc`;
fsl-5.0.8/src/fugue/invwarp:201: ysize=`echo $ysize + 2 | bc`;
fsl-5.0.8/src/fugue/invwarp-202-fi
fsl-5.0.8/src/fugue/invwarp-203-if [ $zmin -ge 2 ] ; then
fsl-5.0.8/src/fugue/invwarp:204: zmin=`echo $zmin - 2 | bc`;
fsl-5.0.8/src/fugue/invwarp:205: zsize=`echo $zsize + 2 | bc`;
fsl-5.0.8/src/fugue/invwarp-206-fi
fsl-5.0.8/src/fugue/invwarp:207:if [ `$FSLDIR/bin/fslval $refvol dim1` -ge `echo "$xmin + $xsize + 2" | bc` ] ; then
fsl-5.0.8/src/fugue/invwarp:208: xsize=`echo $xsize + 2 | bc`;
fsl-5.0.8/src/fugue/invwarp-209-fi
fsl-5.0.8/src/fugue/invwarp:210:if [ `$FSLDIR/bin/fslval $refvol dim2` -ge `echo "$ymin + $ysize + 2" | bc` ] ; then
fsl-5.0.8/src/fugue/invwarp:211: ysize=`echo $ysize + 2 | bc`;
fsl-5.0.8/src/fugue/invwarp-212-fi
fsl-5.0.8/src/fugue/invwarp:213:if [ `$FSLDIR/bin/fslval $refvol dim3` -ge `echo "$zmin + $zsize + 2" | bc` ] ; then
fsl-5.0.8/src/fugue/invwarp:214: zsize=`echo $zsize + 2 | bc`;
fsl-5.0.8/src/fugue/invwarp-215-fi
##############################################
fsl-5.0.8/src/fugue/invwarp-220-# make xminmm version (in mm not voxels)
fsl-5.0.8/src/fugue/invwarp:221:xvox=`$FSLDIR/bin/fslval $refvol pixdim1`;
fsl-5.0.8/src/fugue/invwarp:222:yvox=`$FSLDIR/bin/fslval $refvol pixdim2`;
fsl-5.0.8/src/fugue/invwarp:223:zvox=`$FSLDIR/bin/fslval $refvol pixdim3`;
fsl-5.0.8/src/fugue/invwarp:224:xminmm=`echo "$xmin * $xvox" | bc -l`;
fsl-5.0.8/src/fugue/invwarp:225:yminmm=`echo "$ymin * $yvox" | bc -l`;
fsl-5.0.8/src/fugue/invwarp:226:zminmm=`echo "$zmin * $zvox" | bc -l`;
fsl-5.0.8/src/fugue/invwarp:227:xsizemm=`echo "$xsize * $xvox" | bc -l`;
fsl-5.0.8/src/fugue/invwarp:228:ysizemm=`echo "$ysize * $yvox" | bc -l`;
fsl-5.0.8/src/fugue/invwarp:229:zsizemm=`echo "$zsize * $zvox" | bc -l`;
fsl-5.0.8/src/fugue/invwarp-230-
fsl-5.0.8/src/fugue/invwarp-231-if [ $verbose = yes ] ; then echo "Making tmp directory" ; fi
fsl-5.0.8/src/fugue/invwarp:232:tmpdir=`$FSLDIR/bin/tmpnam`;
fsl-5.0.8/src/fugue/invwarp-233-origdir=$tmpdir;
##############################################
fsl-5.0.8/src/fugue/invwarp-246- stdvol=$FSLDIR/data/standard/MNI152_T1_2mm
fsl-5.0.8/src/fugue/invwarp:247: if [ `$FSLDIR/bin/imtest standard` = 1 ] ; then stdvol=standard; fi
fsl-5.0.8/src/fugue/invwarp-248-fi
##############################################
fsl-5.0.8/src/fugue/invwarp-260-# NEUROLOGICAL FIX
fsl-5.0.8/src/fugue/invwarp:261:if [ `$FSLDIR/bin/fslorient $refvol ` = NEUROLOGICAL ] ; then
fsl-5.0.8/src/fugue/invwarp:262: dim1=`$FSLDIR/bin/fslval $refvol dim1`;
fsl-5.0.8/src/fugue/invwarp:263: transx=`echo " ( $dim1 - 1 - ( $xmin + $xsize - 1 ) ) * $xvox " | bc -l`;
fsl-5.0.8/src/fugue/invwarp-264-else
##############################################
fsl-5.0.8/src/fugue/invwarp-287-warp=$tmpdir/standard2highres_full_warp
fsl-5.0.8/src/fugue/invwarp:288:refdim1=`$FSLDIR/bin/fslval $refvol dim1`;
fsl-5.0.8/src/fugue/invwarp:289:refdim2=`$FSLDIR/bin/fslval $refvol dim2`;
fsl-5.0.8/src/fugue/invwarp:290:refdim3=`$FSLDIR/bin/fslval $refvol dim3`;
fsl-5.0.8/src/fugue/invwarp:291:dim1=`$FSLDIR/bin/fslval $warp dim1`;
fsl-5.0.8/src/fugue/invwarp:292:dim2=`$FSLDIR/bin/fslval $warp dim2`;
fsl-5.0.8/src/fugue/invwarp:293:dim3=`$FSLDIR/bin/fslval $warp dim3`;
fsl-5.0.8/src/fugue/invwarp-294-# extend in z first
##############################################
fsl-5.0.8/src/fugue/invwarp-297-$FSLDIR/bin/fslroi $warp $bottom_slice 0 $dim1 0 $dim2 0 1 0 3
fsl-5.0.8/src/fugue/invwarp:298:$FSLDIR/bin/fslroi $warp $top_slice 0 $dim1 0 $dim2 `echo $dim3 - 1 | bc` 1 0 3
fsl-5.0.8/src/fugue/invwarp-299-com="$FSLDIR/bin/fslmerge -z $warp ";
fsl-5.0.8/src/fugue/invwarp-300-sl=0;
fsl-5.0.8/src/fugue/invwarp:301:while [ $sl -lt $zmin ] ; do com="$com $bottom_slice "; sl=`echo $sl + 1 | bc`; done
fsl-5.0.8/src/fugue/invwarp-302-com="$com $warp ";
fsl-5.0.8/src/fugue/invwarp:303:sl=`echo $zmin + $zsize | bc`;
fsl-5.0.8/src/fugue/invwarp-304-if [ $verbose = yes ] ; then echo Starting slice=$sl and finish=$refdim3 ; fi
fsl-5.0.8/src/fugue/invwarp-305-if [ $verbose = yes ] ; then echo zmin=$zmin and zsize=$zsize ; fi
fsl-5.0.8/src/fugue/invwarp:306:while [ $sl -lt $refdim3 ] ; do com="$com $top_slice "; sl=`echo $sl + 1 | bc`; done
fsl-5.0.8/src/fugue/invwarp-307-#echo $com
fsl-5.0.8/src/fugue/invwarp-308-$com
fsl-5.0.8/src/fugue/invwarp:309:dim3=`$FSLDIR/bin/fslval $warp dim3`;
fsl-5.0.8/src/fugue/invwarp-310-# extend in y next
##############################################
fsl-5.0.8/src/fugue/invwarp-313-$FSLDIR/bin/fslroi $warp $back_slice 0 $dim1 0 1 0 $dim3 0 3
fsl-5.0.8/src/fugue/invwarp:314:$FSLDIR/bin/fslroi $warp $front_slice 0 $dim1 `echo $dim2 - 1 | bc` 1 0 $dim3 0 3
fsl-5.0.8/src/fugue/invwarp-315-com="$FSLDIR/bin/fslmerge -y $warp ";
fsl-5.0.8/src/fugue/invwarp-316-sl=0;
fsl-5.0.8/src/fugue/invwarp:317:while [ $sl -lt $ymin ] ; do com="$com $back_slice "; sl=`echo $sl + 1 | bc`; done
fsl-5.0.8/src/fugue/invwarp-318-com="$com $warp ";
fsl-5.0.8/src/fugue/invwarp:319:sl=`echo $ymin + $ysize | bc`;
fsl-5.0.8/src/fugue/invwarp:320:while [ $sl -lt $refdim2 ] ; do com="$com $front_slice "; sl=`echo $sl + 1 | bc`; done
fsl-5.0.8/src/fugue/invwarp-321-#echo $com
fsl-5.0.8/src/fugue/invwarp-322-$com
fsl-5.0.8/src/fugue/invwarp:323:dim2=`$FSLDIR/bin/fslval $warp dim2`;
fsl-5.0.8/src/fugue/invwarp-324-# extend in x next
##############################################
fsl-5.0.8/src/fugue/invwarp-327-$FSLDIR/bin/fslroi $warp $left_slice 0 1 0 $dim2 0 $dim3 0 3
fsl-5.0.8/src/fugue/invwarp:328:$FSLDIR/bin/fslroi $warp $right_slice `echo $dim1 - 1 | bc` 1 0 $dim2 0 $dim3 0 3
fsl-5.0.8/src/fugue/invwarp-329-lcom=""; rcom=""; com="";
fsl-5.0.8/src/fugue/invwarp-330-sl=0;
fsl-5.0.8/src/fugue/invwarp:331:while [ $sl -lt $xmin ] ; do lcom="$lcom $left_slice "; sl=`echo $sl + 1 | bc`; done
fsl-5.0.8/src/fugue/invwarp:332:sl=`echo $xmin + $xsize | bc`;
fsl-5.0.8/src/fugue/invwarp:333:while [ $sl -lt $refdim1 ] ; do rcom="$rcom $right_slice "; sl=`echo $sl + 1 | bc`; done
fsl-5.0.8/src/fugue/invwarp:334:if [ `$FSLDIR/bin/fslorient $refvol ` = NEUROLOGICAL ] ; then
fsl-5.0.8/src/fugue/invwarp-335- # neurological case
##############################################
fsl-5.0.8/src/fugue/invwarp-342-$com
fsl-5.0.8/src/fugue/invwarp:343:dim1=`$FSLDIR/bin/fslval $warp dim1`;
fsl-5.0.8/src/fugue/invwarp-344-
##############################################
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-79-usage() {
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:80: echo "Usage: `basename $0` <phase_image> <magnitude_image>"
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-81- echo " "
##############################################
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-93-
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:94:if [ `$FSLDIR/bin/imtest $1` -ne 1 ]; then
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-95- echo "$1 not found/not an image file"
##############################################
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-98-
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:99:if [ `$FSLDIR/bin/imtest $2` -ne 1 ]; then
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-100- echo "$2 not found/not an image file"
##############################################
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-103-
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:104:phaseroot=`$FSLDIR/bin/remove_ext $1`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:105:absroot=`$FSLDIR/bin/remove_ext $2`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-106-
##############################################
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-113-# check if voxel sizes seem sensible
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:114:nt=`$FSLDIR/bin/fslval ${absroot}_fixed dim3`;
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:115:ny=`$FSLDIR/bin/fslval ${absroot}_fixed dim2`;
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:116:nx=`$FSLDIR/bin/fslval ${absroot}_fixed dim1`;
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:117:dz=`$FSLDIR/bin/fslval ${absroot}_fixed pixdim3`;
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:118:dy=`$FSLDIR/bin/fslval ${absroot}_fixed pixdim2`;
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:119:dx=`$FSLDIR/bin/fslval ${absroot}_fixed pixdim1`;
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:120:if [ `echo "$dz / $dx < 0.9" | bc -l` -eq 1 ] ; then
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:121: pdz=`$FSLDIR/bin/fslval ${phaseroot}_fixed pixdim3`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-122- echo "Detected unusual z-voxel size of $dz mm in magnitude image"
##############################################
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-131-# (should not be needed if reconstruction from dicom was OK)
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:132:nabs=`$FSLDIR/bin/fslval ${absroot}_fixed dim3`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:133:nphs=`$FSLDIR/bin/fslval ${phaseroot}_fixed dim3`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:134:nphs2=`echo "$nphs * 2" | bc`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps:135:tmpnm=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/fugue/fix_OCMR_fieldmaps-136-if [ $nabs -eq $nphs2 ]; then
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-83- fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:84: echo "Usage: `basename $0` <scanner> <phase_image> <magnitude_image> <out_image> <deltaTE (in ms)> [--nocheck]"
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-85- echo " "
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-91- echo " "
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:92: echo " e.g. `basename $0` SIEMENS images_3_gre_field_mapping images_4_gre_field_mapping fmap_rads 2.65"
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-93-}
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-98- imroot=$1
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:99: nvox=`$FSLDIR/bin/fslstats ${imroot} -v | awk '{ print $1 }'`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:100: nvoxnz=`$FSLDIR/bin/fslstats ${imroot} -V | awk '{ print $1 }'`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:101: if [ X`echo "if ( $nvoxnz / $nvox > 0.90 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-102- echo "Magntiude (abs) image should be brain extracted"
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-129- $FSLDIR/bin/fslmaths ${outim} -mas ${maskim} ${tmpnm}_tmp_fmapmasked
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:130: $FSLDIR/bin/fslmaths ${outim} -sub `$FSLDIR/bin/fslstats ${tmpnm}_tmp_fmapmasked -k ${maskim} -P 50` -mas ${maskim} ${outim} -odt float
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-131-}
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-137- absroot=$2
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:138: outfile=`$FSLDIR/bin/remove_ext $3`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-139- deltaTE=$4
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-142-
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:143: nt=`$FSLDIR/bin/fslval ${phaseroot} dim4`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-144- if [ $nt -ne 2 ] ; then
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-151- if [ $sanitycheck = yes ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:152: rr=`$FSLDIR/bin/fslstats ${phaseroot} -R`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:153: rmin=`echo $rr | awk '{ print $1 }'`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:154: rmax=`echo $rr | awk '{ print $2 }'`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:155: range=`echo $rmax - $rmin | bc -l`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:156: nrange=`echo $range / 6.28 | bc -l`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-157- range_ok=yes;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:158: if [ X`echo "if ( $nrange < 0.9 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-159- range_ok=no;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-160- fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:161: if [ X`echo "if ( $nrange > 1.1 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-162- range_ok=no;
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-182- # create fieldmap
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:183: asym=`echo $deltaTE / 1000 | bc -l`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-184- $FSLDIR/bin/fugue -p $uphaseroot --asym=$asym --mask=$maskim --savefmap=$outfile
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-197- absroot=$2
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:198: outfile=`$FSLDIR/bin/remove_ext $3`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-199- deltaTE=$4
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-206- if [ $sanitycheck = yes ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:207: rr=`$FSLDIR/bin/fslstats ${phaseroot} -R;`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:208: rmin=`echo $rr | awk '{ print $1 }'`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:209: rmax=`echo $rr | awk '{ print $2 }'`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:210: range=`echo $rmax - $rmin | bc -l`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:211: nrange=`echo $range / 4096 | bc -l`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:212: if [ X`echo "if ( $nrange < 2.1 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:213: if [ X`echo "if ($nrange > 1.9) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-214- # MRIcron range is typically twice that of dicom2nifti
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-218- fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:219: if [ X`echo "if ( $nrange < 0.9 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-220- echo "Phase image values do not have expected range"
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-240- # Convert to rads/sec (dTE is echo time difference)
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:241: asym=`echo $dTE / 1000 | bc -l`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-242- $FSLDIR/bin/fslmaths ${tmpnm}_tmp_ph_radians_unwrapped -div $asym ${tmpnm}_tmp_ph_rps -odt float
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-265-
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:266:if [ `$FSLDIR/bin/imtest $2` -ne 1 ]; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-267- echo "$2 not found/not an image file"
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-270-
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:271:if [ `$FSLDIR/bin/imtest $3` -ne 1 ]; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-272- echo "$3 not found/not an image file"
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-275-
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:276:phaseroot=`$FSLDIR/bin/remove_ext $2`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:277:absroot=`$FSLDIR/bin/remove_ext $3`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-278-outfile=${phaseroot}_field_rps
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-279-if [ $# -ge 4 ]; then
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:280: outfile=`$FSLDIR/bin/remove_ext $4`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-281-fi
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-296- badval=false;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:297: if [ X`echo "if ( $dTE < 0.1 ) { 1 }" | bc -l` = X1 ] ; then badval=true; fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:298: if [ X`echo "if ( $dTE > 10.0 ) { 1 }" | bc -l` = X1 ] ; then badval=true; fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-299- if [ $badval = true ] ; then
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-306-
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:307:tmpnm=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-308-
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-317-# check that phase and magnitude images are the same size
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:318:nz=`$FSLDIR/bin/fslval ${absroot} dim3`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:319:ny=`$FSLDIR/bin/fslval ${absroot} dim2`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:320:nx=`$FSLDIR/bin/fslval ${absroot} dim1`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:321:dz=`$FSLDIR/bin/fslval ${absroot} pixdim3`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:322:dy=`$FSLDIR/bin/fslval ${absroot} pixdim2`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:323:dx=`$FSLDIR/bin/fslval ${absroot} pixdim1`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:324:pnz=`$FSLDIR/bin/fslval ${phaseroot} dim3`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:325:pny=`$FSLDIR/bin/fslval ${phaseroot} dim2`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:326:pnx=`$FSLDIR/bin/fslval ${phaseroot} dim1`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:327:pdz=`$FSLDIR/bin/fslval ${phaseroot} pixdim3`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:328:pdy=`$FSLDIR/bin/fslval ${phaseroot} pixdim2`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:329:pdx=`$FSLDIR/bin/fslval ${phaseroot} pixdim1`;
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-330-samesize=true;
##############################################
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-333-if [ $nx -ne $pnx ] ; then samesize=false; fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:334:if [ X`echo "if ( $dz != $pdz ) { 1 }" | bc -l` = X1 ] ; then samesize=false; fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:335:if [ X`echo "if ( $dy != $pdy ) { 1 }" | bc -l` = X1 ] ; then samesize=false; fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap:336:if [ X`echo "if ( $dx != $pdx ) { 1 }" | bc -l` = X1 ] ; then samesize=false; fi
fsl-5.0.8/src/fugue/fsl_prepare_fieldmap-337-if [ $samesize = false ] ; then
##############################################
fsl-5.0.8/src/fugue/extractfidparams-77- echo " "
fsl-5.0.8/src/fugue/extractfidparams:78: echo "Usage: `basename $0` fid_directory"
fsl-5.0.8/src/fugue/extractfidparams-79- exit -1
##############################################
fsl-5.0.8/src/fugue/extractfidparams-89-# for a fieldmap
fsl-5.0.8/src/fugue/extractfidparams:90:asym=`extracttxt '^asym[^a-z0-9]' $fmap/procpar 1 1 | cut -d' ' -f3`
fsl-5.0.8/src/fugue/extractfidparams-91-if [ X${asym}X != XX ] ; then
##############################################
fsl-5.0.8/src/fugue/extractfidparams-98-# otherwise it is a normal epi
fsl-5.0.8/src/fugue/extractfidparams:99:np=`extracttxt '^np[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams:100:sw=`extracttxt '^sw[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams:101:lro=`extracttxt '^lro[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams:102:gmax=`extracttxt '^gmax[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams:103:echo_del=`extracttxt '^echo_del[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams:104:num_ints=`extracttxt '^num_ints[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams:105:grise=`extracttxt '^grise_copy[^a-z0-9]' $epi/procpar 1 1 | cut -d' ' -f2`
fsl-5.0.8/src/fugue/extractfidparams-106-if [ X${grise}X = XX ] ; then grise=0; fi
##############################################
fsl-5.0.8/src/fugue/extractfidparams-110-
fsl-5.0.8/src/fugue/extractfidparams:111:tau_pe=`echo "12 k $np 2.0 / $sw / 2.0 $sw * $grise * $lro / 4257.5 / $gmax / $echo_del 1000000 / + + $num_ints / p" | dc`;
fsl-5.0.8/src/fugue/extractfidparams-112-
##############################################
fsl-5.0.8/src/fugue/fixpiramps.sh-74-
fsl-5.0.8/src/fugue/fixpiramps.sh:75:arg1=`$FSLDIR/bin/remove_ext $1`
fsl-5.0.8/src/fugue/fixpiramps.sh-76-
fsl-5.0.8/src/fugue/fixpiramps.sh:77:dtype=`$FSLDIR/bin/fslval $arg1 datatype`;
fsl-5.0.8/src/fugue/fixpiramps.sh-78-if [ $dtype -eq 32 ] ; then
##############################################
fsl-5.0.8/src/fugue/fixpiramps.sh-89-tt=0;
fsl-5.0.8/src/fugue/fixpiramps.sh:90:tmax=`fslval $arg1 dim4`;
fsl-5.0.8/src/fugue/fixpiramps.sh-91-
##############################################
fsl-5.0.8/src/fugue/fixpiramps.sh-97- if [ $tt -eq 0 ] ; then
fsl-5.0.8/src/fugue/fixpiramps.sh:98: xdim=`$FSLDIR/bin/fslval $phaseim pixdim1`;
fsl-5.0.8/src/fugue/fixpiramps.sh:99: ydim=`$FSLDIR/bin/fslval $phaseim pixdim2`;
fsl-5.0.8/src/fugue/fixpiramps.sh:100: zdim=`$FSLDIR/bin/fslval $phaseim pixdim3`;
fsl-5.0.8/src/fugue/fixpiramps.sh-101-
fsl-5.0.8/src/fugue/fixpiramps.sh:102: pixdim=`echo "scale=10; $xdim / 3.14159265 " | bc`;
fsl-5.0.8/src/fugue/fixpiramps.sh:103: piydim=`echo "scale=10; $ydim / 3.14159265 " | bc`;
fsl-5.0.8/src/fugue/fixpiramps.sh:104: pizdim=`echo "scale=10; $zdim / 3.14159265 " | bc`;
fsl-5.0.8/src/fugue/fixpiramps.sh-105-
##############################################
fsl-5.0.8/src/fugue/fixpiramps.sh-144-
fsl-5.0.8/src/fugue/fixpiramps.sh:145: tt=`echo $tt + 1 | bc`;
fsl-5.0.8/src/fugue/fixpiramps.sh-146- # end while loop
##############################################
fsl-5.0.8/src/first/first_boundary_corr-73- echo ""
fsl-5.0.8/src/first/first_boundary_corr:74: echo "Usage: `basename $0` -s <segmented_image> -i <intensity_image> -o <output_image> -b <boundary_correction_method> [options]"
fsl-5.0.8/src/first/first_boundary_corr-75- echo ""
##############################################
fsl-5.0.8/src/first/first_boundary_corr-79- echo ""
fsl-5.0.8/src/first/first_boundary_corr:80: echo "e.g.: `basename $0` -s image_first_L_Hipp -i orig_t1 -o image_first_L_Hipp_corr -b fast"
fsl-5.0.8/src/first/first_boundary_corr-81- exit 1
##############################################
fsl-5.0.8/src/first/first_boundary_corr-104- $FSLDIR/bin/fslmaths ${imlb} -uthr 100 ${imout}_grot
fsl-5.0.8/src/first/first_boundary_corr:105: lb=`fslstats ${imout}_grot -R | awk '{ print $2 }'`
fsl-5.0.8/src/first/first_boundary_corr-106- ${FSLDIR}/bin/imrm ${imout}_grot
fsl-5.0.8/src/first/first_boundary_corr-107-
fsl-5.0.8/src/first/first_boundary_corr:108: xvox=`$FSLDIR/bin/fslval ${imlb} pixdim1`
fsl-5.0.8/src/first/first_boundary_corr:109: yvox=`$FSLDIR/bin/fslval ${imlb} pixdim2`
fsl-5.0.8/src/first/first_boundary_corr:110: zvox=`$FSLDIR/bin/fslval ${imlb} pixdim3`
fsl-5.0.8/src/first/first_boundary_corr-111-
fsl-5.0.8/src/first/first_boundary_corr:112: bounds=`$FSLDIR/bin/fslstats $imlb -w`
fsl-5.0.8/src/first/first_boundary_corr-113- if [ $verbose = yes ] ; then echo "Initial bounds: $bounds" ; fi;
fsl-5.0.8/src/first/first_boundary_corr-114-
fsl-5.0.8/src/first/first_boundary_corr:115: xmin=`echo $bounds | awk '{ print $1 }'`
fsl-5.0.8/src/first/first_boundary_corr:116: xsize=`echo $bounds | awk '{ print $2 }'`
fsl-5.0.8/src/first/first_boundary_corr:117: ymin=`echo $bounds | awk '{ print $3 }'`
fsl-5.0.8/src/first/first_boundary_corr:118: ysize=`echo $bounds | awk '{ print $4 }'`
fsl-5.0.8/src/first/first_boundary_corr:119: zmin=`echo $bounds | awk '{ print $5 }'`
fsl-5.0.8/src/first/first_boundary_corr:120: zsize=`echo $bounds | awk '{ print $6 }'`
fsl-5.0.8/src/first/first_boundary_corr-121-
##############################################
fsl-5.0.8/src/first/first_boundary_corr-123-
fsl-5.0.8/src/first/first_boundary_corr:124: xmin=`echo "${xmin} - $offset" | bc`
fsl-5.0.8/src/first/first_boundary_corr:125: xsize=`echo "$xsize + 2*$offset" | bc`
fsl-5.0.8/src/first/first_boundary_corr:126: ymin=`echo "$ymin - $offset" | bc`
fsl-5.0.8/src/first/first_boundary_corr:127: ysize=`echo "$ysize + 2*$offset" | bc`
fsl-5.0.8/src/first/first_boundary_corr:128: zmin=`echo "$zmin - $offset" | bc`
fsl-5.0.8/src/first/first_boundary_corr:129: zsize=`echo "$zsize + 2*$offset" | bc`
fsl-5.0.8/src/first/first_boundary_corr-130- if [ $verbose = yes ] ; then echo "fslroi call with : $xmin $xsize $ymin $ysize $zmin $zsize"; fi;
##############################################
fsl-5.0.8/src/first/first_boundary_corr-139- $FSLDIR/bin/fslmaths ${imout}_lb_roi -bin -mul ${imout}_t1_roi_seg ${imout}_lb_roi_seg
fsl-5.0.8/src/first/first_boundary_corr:140: greylb=`$FSLDIR/bin/fslstats ${imout}_lb_roi_seg -M`
fsl-5.0.8/src/first/first_boundary_corr-141-
fsl-5.0.8/src/first/first_boundary_corr-142- if [ $verbose = yes ] ; then echo "Pre-round $greylb" ; fi;
fsl-5.0.8/src/first/first_boundary_corr:143: greylb=`echo $greylb + 0.5 | bc -l | sed 's/\.[0-9]*//'`; # round the value (sed truncates from decimal place)
fsl-5.0.8/src/first/first_boundary_corr-144- if [ $verbose = yes ] ; then echo "Post-round $greylb" ; fi;
##############################################
fsl-5.0.8/src/first/first_boundary_corr-150- # having processed the rois, now put them back into the larger images
fsl-5.0.8/src/first/first_boundary_corr:151: transx=`echo $xmin \* $xvox | bc -l`;
fsl-5.0.8/src/first/first_boundary_corr:152: transy=`echo $ymin \* $yvox | bc -l`;
fsl-5.0.8/src/first/first_boundary_corr:153: transz=`echo $zmin \* $zvox | bc -l`;
fsl-5.0.8/src/first/first_boundary_corr-154- # deal with annoying flip of x coordinates for FLIRT conventions in neuro
fsl-5.0.8/src/first/first_boundary_corr:155: if [ `$FSLDIR/bin/fslorient $imlb ` = NEUROLOGICAL ] ; then
fsl-5.0.8/src/first/first_boundary_corr:156: dim1=`$FSLDIR/bin/fslval $imlb dim1`
fsl-5.0.8/src/first/first_boundary_corr:157: transx=`echo " ( $dim1 - 1 - ( $xmin + $xsize - 1 ) ) * $xvox" | bc -l`;
fsl-5.0.8/src/first/first_boundary_corr-158- fi
##############################################
fsl-5.0.8/src/first/first_boundary_corr-175-export GETOPT_COMPATIBLE POSIXLY_CORRECT
fsl-5.0.8/src/first/first_boundary_corr:176:args=`getopt s:i:o:b:t:v $*`
fsl-5.0.8/src/first/first_boundary_corr-177-if [ $? != 0 ] || [ $# -eq 0 ] ; then
##############################################
fsl-5.0.8/src/first/first_boundary_corr-209-
fsl-5.0.8/src/first/first_boundary_corr:210:if [ `${FSLDIR}/bin/imtest $segim` = 0 ] ; then
fsl-5.0.8/src/first/first_boundary_corr-211- echo "Error: cannot find image $segim"
##############################################
fsl-5.0.8/src/first/first_boundary_corr-213-fi
fsl-5.0.8/src/first/first_boundary_corr:214:segim=`${FSLDIR}/bin/remove_ext $segim`
fsl-5.0.8/src/first/first_boundary_corr-215-
fsl-5.0.8/src/first/first_boundary_corr:216:if [ `${FSLDIR}/bin/imtest $intim` = 0 ] ; then
fsl-5.0.8/src/first/first_boundary_corr-217- echo "Error: cannot find image $intim"
##############################################
fsl-5.0.8/src/first/first_boundary_corr-219-fi
fsl-5.0.8/src/first/first_boundary_corr:220:intim=`${FSLDIR}/bin/remove_ext $intim`
fsl-5.0.8/src/first/first_boundary_corr-221-
##############################################
fsl-5.0.8/src/first/first3Dview-72-if [ $# -lt 2 ] ; then
fsl-5.0.8/src/first/first3Dview:73: echo "`basename $0` <mask image> <corrp image>"
fsl-5.0.8/src/first/first3Dview-74- exit 1
##############################################
fsl-5.0.8/src/first/first3Dview-79-
fsl-5.0.8/src/first/first3Dview:80:basename=`$FSLDIR/bin/remove_ext $2`
fsl-5.0.8/src/first/first3Dview-81-#calculate filled structure
##############################################
fsl-5.0.8/src/first/first3Dview-83-$FSLDIR/bin/cluster -t 0.5 -i ${basename}_invmask -o ${basename}_invmask_comps --connectivity=6 --no_table
fsl-5.0.8/src/first/first3Dview:84:maxc=`$FSLDIR/bin/fslstats ${basename}_invmask_comps -P 100`
fsl-5.0.8/src/first/first3Dview:85:maxc1=`echo $maxc -1 | bc`
fsl-5.0.8/src/first/first3Dview-86-$FSLDIR/bin/fslmaths ${basename}_invmask_comps -uthr $maxc1 -thr 1 -add $maskim -bin ${basename}_filledstruct
##############################################
fsl-5.0.8/src/first/run_first_all-73- echo ""
fsl-5.0.8/src/first/run_first_all:74: echo "Usage: `basename $0` [options] -i <input_image> -o <output_image>"
fsl-5.0.8/src/first/run_first_all-75- echo ""
##############################################
fsl-5.0.8/src/first/run_first_all-85- echo ""
fsl-5.0.8/src/first/run_first_all:86: echo "e.g.: `basename $0` -i im1 -o output_name "
fsl-5.0.8/src/first/run_first_all-87- exit 1
##############################################
fsl-5.0.8/src/first/run_first_all-109-else
fsl-5.0.8/src/first/run_first_all:110: args=`getopt i:o:m:s:a:bd3vh $*`
fsl-5.0.8/src/first/run_first_all-111- if [ $? != 0 ] ; then
##############################################
fsl-5.0.8/src/first/run_first_all-152- -s)
fsl-5.0.8/src/first/run_first_all:153: structs=`echo "$2" | sed 's/,/ /g'`;
fsl-5.0.8/src/first/run_first_all-154- shift 2;;
##############################################
fsl-5.0.8/src/first/run_first_all-158-
fsl-5.0.8/src/first/run_first_all:159:if [ `${FSLDIR}/bin/imtest $iname` = 0 ] ; then
fsl-5.0.8/src/first/run_first_all-160- echo "Error: cannot find image $iname"
##############################################
fsl-5.0.8/src/first/run_first_all-162-fi
fsl-5.0.8/src/first/run_first_all:163:iname=`${FSLDIR}/bin/remove_ext $iname`
fsl-5.0.8/src/first/run_first_all-164-
##############################################
fsl-5.0.8/src/first/run_first_all-172-
fsl-5.0.8/src/first/run_first_all:173:oname=`$FSLDIR/bin/remove_ext $oname`;
fsl-5.0.8/src/first/run_first_all-174-
##############################################
fsl-5.0.8/src/first/run_first_all-183-if [ $doReg = yes ] ; then
fsl-5.0.8/src/first/run_first_all:184: if [ -w `dirname $iname` ] ; then
fsl-5.0.8/src/first/run_first_all-185- matname=${iname}_to_std_sub;
##############################################
fsl-5.0.8/src/first/run_first_all-192- if [ $verbose = yes ] ; then echo ${FSLDIR}/bin/first_flirt $iname ${matname} $flirtopts ; fi
fsl-5.0.8/src/first/run_first_all:193: FLIRTID=`${FSLDIR}/bin/fsl_sub -l $logdir -T 15 ${FSLDIR}/bin/first_flirt $iname ${matname} $flirtopts`
fsl-5.0.8/src/first/run_first_all-194- FLIRTJOBHOLD="-j $FLIRTID"
##############################################
fsl-5.0.8/src/first/run_first_all-206- intref=0;
fsl-5.0.8/src/first/run_first_all:207: S_FIRST_4=`awk 'BEGIN {print substr("'$s'",3,4)}'`
fsl-5.0.8/src/first/run_first_all-208- case "${S_FIRST_4}" in
##############################################
fsl-5.0.8/src/first/run_first_all-262- else
fsl-5.0.8/src/first/run_first_all:263: S_CUT=`awk 'BEGIN {print substr("'$s'",1,1)}'`
fsl-5.0.8/src/first/run_first_all-264- ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/run_first -i $iname -t ${affmat} -n $nmodes -o ${imfirst} -m ${FSLDIR}/data/first/models_${modelN}_bin/intref_thal/${s}.bmv -intref ${FSLDIR}/data/first/models_336_bin/05mm/${S_CUT}_Thal_05mm.bmv\c" >> $COM
##############################################
fsl-5.0.8/src/first/run_first_all-281-if [ $verbose = yes ] ; then cat $COM ; fi
fsl-5.0.8/src/first/run_first_all:282:FIRSTID=`${FSLDIR}/bin/fsl_sub -l $logdir -T 60 -N first $FLIRTJOBHOLD -t $COM`
fsl-5.0.8/src/first/run_first_all-283-
fsl-5.0.8/src/first/run_first_all-284-if [ $btype = thresh ] ; then
fsl-5.0.8/src/first/run_first_all:285: threshnop=`echo $thresh | sed 's/\.//g'`
fsl-5.0.8/src/first/run_first_all-286- methname=th${threshnop} ;
##############################################
fsl-5.0.8/src/first/run_first_all-290-
fsl-5.0.8/src/first/run_first_all:291:numstruct=`echo $structs | wc -w`;
fsl-5.0.8/src/first/run_first_all-292-if [ $numstruct -gt 1 ] ; then
##############################################
fsl-5.0.8/src/first/run_first_all-294- if [ $verbose = yes ] ; then cat ${COM}2 ; fi
fsl-5.0.8/src/first/run_first_all:295: MERGEID=`$FSLDIR/bin/fsl_sub -l $logdir -T 15 -N first_post -j $FIRSTID -t ${COM}2`
fsl-5.0.8/src/first/run_first_all-296- MERGEHOLD="-j $MERGEID"
##############################################
fsl-5.0.8/src/first/first_roi_slicesdir-86-echo "total number of image: " $num
fsl-5.0.8/src/first/first_roi_slicesdir:87:num=`echo "${num}/2 " | bc`
fsl-5.0.8/src/first/first_roi_slicesdir-88-echo "number of image pairs: " $num
##############################################
fsl-5.0.8/src/first/first_roi_slicesdir-93-
fsl-5.0.8/src/first/first_roi_slicesdir:94: pout=`echo $@ | awk '{ print $'$i' }'`
fsl-5.0.8/src/first/first_roi_slicesdir-95-
fsl-5.0.8/src/first/first_roi_slicesdir:96: imind=`echo ${i} + ${num} | bc`
fsl-5.0.8/src/first/first_roi_slicesdir:97: imlb=`echo $@ | awk '{ print $'$imind' }'`
fsl-5.0.8/src/first/first_roi_slicesdir:98: imlbout=`echo $imlb | awk -F / '{ print $NF }'`
fsl-5.0.8/src/first/first_roi_slicesdir:99: imlbout=`remove_ext $imlbout `
fsl-5.0.8/src/first/first_roi_slicesdir-100-
fsl-5.0.8/src/first/first_roi_slicesdir:101: roi=`${FSLDIR}/bin/fslstats $imlb -w`
fsl-5.0.8/src/first/first_roi_slicesdir-102-
fsl-5.0.8/src/first/first_roi_slicesdir:103: xmin=`echo $roi | awk '{ print $1 }'`
fsl-5.0.8/src/first/first_roi_slicesdir:104: xsize=`echo $roi | awk '{ print $2 }'`
fsl-5.0.8/src/first/first_roi_slicesdir:105: xmin=`echo $xmin - 10 | bc`
fsl-5.0.8/src/first/first_roi_slicesdir:106: xsize=`echo $xsize + 20 | bc`
fsl-5.0.8/src/first/first_roi_slicesdir-107-
fsl-5.0.8/src/first/first_roi_slicesdir-108-
fsl-5.0.8/src/first/first_roi_slicesdir:109: ymin=`echo $roi | awk '{ print $3 }'`
fsl-5.0.8/src/first/first_roi_slicesdir:110: ysize=`echo $roi | awk '{ print $4 }'`
fsl-5.0.8/src/first/first_roi_slicesdir:111: ymin=`echo $ymin - 10 | bc`
fsl-5.0.8/src/first/first_roi_slicesdir:112: ysize=`echo $ysize + 20 | bc`
fsl-5.0.8/src/first/first_roi_slicesdir-113-
fsl-5.0.8/src/first/first_roi_slicesdir:114: zmin=`echo $roi | awk '{ print $5 }'`
fsl-5.0.8/src/first/first_roi_slicesdir:115: zsize=`echo $roi | awk '{ print $6 }'`
fsl-5.0.8/src/first/first_roi_slicesdir:116: zmin=`echo $zmin - 10 | bc`
fsl-5.0.8/src/first/first_roi_slicesdir:117: zsize=`echo $zsize + 20 | bc`
fsl-5.0.8/src/first/first_roi_slicesdir-118-
##############################################
fsl-5.0.8/src/first/first_roi_slicesdir-120-
fsl-5.0.8/src/first/first_roi_slicesdir:121: pout=`remove_ext $pout`
fsl-5.0.8/src/first/first_roi_slicesdir:122: imlb=`remove_ext $imlb`
fsl-5.0.8/src/first/first_roi_slicesdir-123-
fsl-5.0.8/src/first/first_roi_slicesdir:124: pout2=`echo $pout | awk -F / '{ print $NF }'`
fsl-5.0.8/src/first/first_roi_slicesdir:125: pout2=`remove_ext $pout2`
fsl-5.0.8/src/first/first_roi_slicesdir-126- echo $i $pout2
##############################################
fsl-5.0.8/src/first/run_first-95- elif [ $1 = -m ] ; then
fsl-5.0.8/src/first/run_first:96: required=`echo $required + 1 | bc`
fsl-5.0.8/src/first/run_first-97- model=$2
##############################################
fsl-5.0.8/src/first/run_first-99- elif [ $1 = -t ] ; then
fsl-5.0.8/src/first/run_first:100: required=`echo $required + 1 | bc`
fsl-5.0.8/src/first/run_first-101- trmat=$2
##############################################
fsl-5.0.8/src/first/run_first-103- elif [ $1 = -i ] ; then
fsl-5.0.8/src/first/run_first:104: required=`echo $required + 1 | bc`
fsl-5.0.8/src/first/run_first:105: image=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/first/run_first-106- shift 2
fsl-5.0.8/src/first/run_first-107- elif [ $1 = -n ] ; then
fsl-5.0.8/src/first/run_first:108: required=`echo $required + 1 | bc`
fsl-5.0.8/src/first/run_first-109- modes=$2
##############################################
fsl-5.0.8/src/first/run_first-123- elif [ $1 = -o ] ; then
fsl-5.0.8/src/first/run_first:124: required=`echo $required + 1 | bc`
fsl-5.0.8/src/first/run_first-125- outname=$2
##############################################
fsl-5.0.8/src/first/run_first-139-else
fsl-5.0.8/src/first/run_first:140:[ `${FSLDIR}/bin/imtest $image` = 0 ] && Usage
fsl-5.0.8/src/first/run_first-141-[ ${required} -ne 5 ] && Usage
##############################################
fsl-5.0.8/src/first/surface_fdr-73-if [ $# -lt 1 ] ; then
fsl-5.0.8/src/first/surface_fdr:74: echo "Usage: `basename $0` <input_vtk>"
fsl-5.0.8/src/first/surface_fdr-75- echo " where input_vtk is the vertex analysis vtk output"
##############################################
fsl-5.0.8/src/first/surface_fdr-78-# echo " For FSL4.1.2 or before:"
fsl-5.0.8/src/first/surface_fdr:79:# echo " `basename $0` <input vtk> <dof> <dof2>"
fsl-5.0.8/src/first/surface_fdr-80-# echo " For the second usage the two Degrees Of Freedom for the"
##############################################
fsl-5.0.8/src/first/surface_fdr-85-
fsl-5.0.8/src/first/surface_fdr:86:infile=`echo $1 | sed 's/.vtk$//'`;
fsl-5.0.8/src/first/surface_fdr-87-
##############################################
fsl-5.0.8/src/first/surface_fdr-92- txtfile=$2
fsl-5.0.8/src/first/surface_fdr:93: dof=`cat ${txtfile} | grep -i pillai | head -1 | awk '{ print $5 }'`;
fsl-5.0.8/src/first/surface_fdr:94: dof2=`cat ${txtfile} | grep -i pillai | head -1 | awk '{ print $6 }'`;
fsl-5.0.8/src/first/surface_fdr-95- echo "Degrees of freedom are: $dof $dof2"
##############################################
fsl-5.0.8/src/first/surface_fdr-105-$FSLDIR/bin/run_mesh_utils -m ${infile}_pvals.vtk -o ${infile}_pvals --doScalarsToVolume
fsl-5.0.8/src/first/surface_fdr:106:thr=`$FSLDIR/bin/fdr -i ${infile}_pvals -q 0.05 | grep -v '^ *[A-Za-z]'`;
fsl-5.0.8/src/first/surface_fdr-107-echo "FDR threshold is $thr"
##############################################
fsl-5.0.8/src/first/concat_bvars-100-
fsl-5.0.8/src/first/concat_bvars:101:listfile=`$FSLDIR/bin/tmpnam`_bvars
fsl-5.0.8/src/first/concat_bvars-102-if [ -f ${listfile}.txt ] ; then rm -f ${listfile}.txt ; fi
##############################################
fsl-5.0.8/src/first/first_flirt-88-[ "$2" = "" ] && Usage
fsl-5.0.8/src/first/first_flirt:89:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/first/first_flirt:90:A=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/first/first_flirt:91:B=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/first/first_flirt-92-shift 2
##############################################
fsl-5.0.8/src/basil/basil-74- echo "Bayesian Inference for Arterial Spin Labelling MRI"
fsl-5.0.8/src/basil/basil:75: echo "Version (build `cat $FSLDIR/etc/fslversion | sed 's/\.//g'`)"
fsl-5.0.8/src/basil/basil-76- echo ""
##############################################
fsl-5.0.8/src/basil/basil-180- outdir=$outdir"+"
fsl-5.0.8/src/basil/basil:181: count=`expr $count + 1`
fsl-5.0.8/src/basil/basil-182-
##############################################
fsl-5.0.8/src/basil/basil-217-# deal with model specification
fsl-5.0.8/src/basil/basil:218:modelsearch=`grep "model=" $options` #look for model in options file (the placement of the model in the options file is to be DEPRECEATED)
fsl-5.0.8/src/basil/basil:219:modelsearch=`echo $modelsearch | sed 's/'".*\(--model=[a-z]*\).*"'/\1/'` #if there are multple options on one line
fsl-5.0.8/src/basil/basil-220-#echo $modelsearch
##############################################
fsl-5.0.8/src/basil/basil-226- if [ -z $model ]; then
fsl-5.0.8/src/basil/basil:227: model=`echo $modelsearch | sed s/--model=//`
fsl-5.0.8/src/basil/basil-228- else
##############################################
fsl-5.0.8/src/basil/basil-246-# get tau value from $options (if set)
fsl-5.0.8/src/basil/basil:247:tausearch=`grep tau $options`
fsl-5.0.8/src/basil/basil:248:tausearch=`echo $tausearch | sed 's:.*--tau=\([0-9]*.[0-9]*\).*:\1:'`
fsl-5.0.8/src/basil/basil-249-if [ ! -z $tausearch ]; then
##############################################
fsl-5.0.8/src/basil/basil-293- stepfromtext="- init with STEP $stepfrom"
fsl-5.0.8/src/basil/basil:294: step=`expr $step + 1`
fsl-5.0.8/src/basil/basil-295-
##############################################
fsl-5.0.8/src/basil/basil-311- stepfrom=$step
fsl-5.0.8/src/basil/basil:312: step=`expr $step + 1`
fsl-5.0.8/src/basil/basil-313-fi
##############################################
fsl-5.0.8/src/basil/basil-337- stepfrom=$step
fsl-5.0.8/src/basil/basil:338: step=`expr $step + 1`
fsl-5.0.8/src/basil/basil-339- fi
##############################################
fsl-5.0.8/src/basil/basil-348- insposn=3 #sets position for tissue tau to be inserted by mvntool
fsl-5.0.8/src/basil/basil:349: nparam=`expr $nparam + 1`
fsl-5.0.8/src/basil/basil-350- paramtext=$paramtext", tau"
##############################################
fsl-5.0.8/src/basil/basil-356- btau_spriors=$btau_spriors"${BLstype}"
fsl-5.0.8/src/basil/basil:357: nparam=`expr $nparam + 1`
fsl-5.0.8/src/basil/basil-358- fi
##############################################
fsl-5.0.8/src/basil/basil-377- stepfrom=$step
fsl-5.0.8/src/basil/basil:378: step=`expr $step + 1`
fsl-5.0.8/src/basil/basil-379- fi
##############################################
fsl-5.0.8/src/basil/basil-384-if [ ! -z $inferwm ]; then
fsl-5.0.8/src/basil/basil:385: insposn=`expr $nparam + 1`
fsl-5.0.8/src/basil/basil:386: nparam=`expr $nparam + 2`
fsl-5.0.8/src/basil/basil-387- nwmparam=2
##############################################
fsl-5.0.8/src/basil/basil-392- if [ ! -z $infertau ]; then
fsl-5.0.8/src/basil/basil:393: nparam=`expr $nparam + 1`
fsl-5.0.8/src/basil/basil:394: nwmparam=`expr $nwmparam + 1`
fsl-5.0.8/src/basil/basil-395- paramtext=$paramtext", wmtau"
##############################################
fsl-5.0.8/src/basil/basil-404- $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=$insposn --new --val=1 --var=1
fsl-5.0.8/src/basil/basil:405: $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=`expr $insposn + 1` --new --val=1 --var=0.1
fsl-5.0.8/src/basil/basil-406-
fsl-5.0.8/src/basil/basil-407- if [ ! -z $infertau ]; then
fsl-5.0.8/src/basil/basil:408: $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=`expr $insposn + 2` --new --val=$tauset --var=0.1
fsl-5.0.8/src/basil/basil-409- fi
##############################################
fsl-5.0.8/src/basil/basil-415- stepfrom=$step
fsl-5.0.8/src/basil/basil:416: step=`expr $step + 1`
fsl-5.0.8/src/basil/basil-417- fi
##############################################
fsl-5.0.8/src/basil/basil-423-# STEP: VB add variable T1
fsl-5.0.8/src/basil/basil:424: insposn=`expr $nparam + 1` # sets postion for T1 parameters to be inserted by mvntool
fsl-5.0.8/src/basil/basil-425- ### (NB btau is put at very end - so we have to adjust if it is in there)
fsl-5.0.8/src/basil/basil-426- if [ ! -z infertau -a ! -z inferart ]; then
fsl-5.0.8/src/basil/basil:427: insposn=`expr $insposn - 1`
fsl-5.0.8/src/basil/basil-428- fi
fsl-5.0.8/src/basil/basil-429-
fsl-5.0.8/src/basil/basil:430: nparam=`expr $nparam + 2`
fsl-5.0.8/src/basil/basil-431- paramtext=$paramtext", T1, T1b"
##############################################
fsl-5.0.8/src/basil/basil-442- # need to correct insertion position for the WM parameters that have been added to the very end
fsl-5.0.8/src/basil/basil:443: insposn=`expr $insposn - 2`
fsl-5.0.8/src/basil/basil-444- if [ ! -z $infertau ]; then
fsl-5.0.8/src/basil/basil:445: insposn=`expr $insposn - 1`
fsl-5.0.8/src/basil/basil-446- fi
##############################################
fsl-5.0.8/src/basil/basil-448- #deal with WM T1
fsl-5.0.8/src/basil/basil:449: nparam=`expr $nparam + 1`
fsl-5.0.8/src/basil/basil:450: nwmparam=`expr $nwmparam + 1`
fsl-5.0.8/src/basil/basil-451- paramtext=$paramtext", T1wm"
##############################################
fsl-5.0.8/src/basil/basil-462- $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=$insposn --new --val=1.3 --var=0.01
fsl-5.0.8/src/basil/basil:463: $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=`expr $insposn + 1` --new --val=1.6 --var=0.01
fsl-5.0.8/src/basil/basil-464- # (NB we dont worry about the T1t image here, we will overwrite this parameter later
##############################################
fsl-5.0.8/src/basil/basil-475- stepfrom=$step
fsl-5.0.8/src/basil/basil:476: step=`expr $step + 1`
fsl-5.0.8/src/basil/basil-477- fi
##############################################
fsl-5.0.8/src/basil/basil-489-
fsl-5.0.8/src/basil/basil:490: nbaseparam=`expr $nparam - $nwmparam` # number of base parameters - excluding those from the WM component
fsl-5.0.8/src/basil/basil-491- # need this to set the spatial priors string
##############################################
fsl-5.0.8/src/basil/basil-507- #spriors=$spriors"${stype}${ATstype}"
fsl-5.0.8/src/basil/basil:508: gmparam=`echo ${#spriors}` #gmparam is position of GM image prior in string
fsl-5.0.8/src/basil/basil:509: gmparam=`expr $gmparam + 1`
fsl-5.0.8/src/basil/basil-510-
##############################################
fsl-5.0.8/src/basil/basil-512- #spriors=$spriors"N"
fsl-5.0.8/src/basil/basil:513: #gmparam=`expr $gmparam + 1`
fsl-5.0.8/src/basil/basil-514- #fi
##############################################
fsl-5.0.8/src/basil/basil-516- #spriors=$spriors"N"
fsl-5.0.8/src/basil/basil:517: #gmparam=`expr $gmparam + 1`
fsl-5.0.8/src/basil/basil-518- #fi
##############################################
fsl-5.0.8/src/basil/basil-534- if [ ! -z $pvcorr ]; then
fsl-5.0.8/src/basil/basil:535: wmparam=`expr $gmparam + 1`
fsl-5.0.8/src/basil/basil-536- extras=$extras" --image-prior${gmparam}=$pgm --image-prior${wmparam}=$pwm"
##############################################
fsl-5.0.8/src/basil/basil-556- # add fixed PV values to the MVN otherwise fabber will fail
fsl-5.0.8/src/basil/basil:557: insposn=`expr $nparam + 1`
fsl-5.0.8/src/basil/basil-558- $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=$insposn --new --valim=$pgm --var=1e-12
fsl-5.0.8/src/basil/basil:559: $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=`expr $insposn + 1` --new --valim=$pwm --var=1e-12
fsl-5.0.8/src/basil/basil-560-
##############################################
fsl-5.0.8/src/basil/basil-574- $mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=fwm --param-list=$outdir/nextstep/paramnames.txt --write --valim=$outdir/wmcbf_init --var=0.1
fsl-5.0.8/src/basil/basil:575: #wmposn=`expr $nparam - 1` #-1 for WM BAT (NB PV maps have not been counted)
fsl-5.0.8/src/basil/basil:576: #if [ ! -z $infertau ]; then wmposn=`expr $wmposn - 1`; fi
fsl-5.0.8/src/basil/basil:577: #if [ ! -z $infert1 ]; then wmposn=`expr $wmposn - 1`; fi
fsl-5.0.8/src/basil/basil-578- #$mvntool --input=$outdir/temp --output=$outdir/temp --mask=$mask --param=$wmposn --write --val=20
##############################################
fsl-5.0.8/src/basil/basil_var-102-
fsl-5.0.8/src/basil/basil_var:103:steps=`ls -d $datdir/step[0-9]`
fsl-5.0.8/src/basil/basil_var-104-
##############################################
fsl-5.0.8/src/melodic/dual_regression-104-
fsl-5.0.8/src/melodic/dual_regression:105:ICA_MAPS=`${FSLDIR}/bin/remove_ext $1` ; shift
fsl-5.0.8/src/melodic/dual_regression-106-
##############################################
fsl-5.0.8/src/melodic/dual_regression-123-
fsl-5.0.8/src/melodic/dual_regression:124:OUTPUT=`${FSLDIR}/bin/remove_ext $1` ; shift
fsl-5.0.8/src/melodic/dual_regression-125-
fsl-5.0.8/src/melodic/dual_regression-126-while [ _$1 != _ ] ; do
fsl-5.0.8/src/melodic/dual_regression:127: INPUTS="$INPUTS `${FSLDIR}/bin/remove_ext $1`"
fsl-5.0.8/src/melodic/dual_regression-128- shift
##############################################
fsl-5.0.8/src/melodic/dual_regression-144-for i in $INPUTS ; do
fsl-5.0.8/src/melodic/dual_regression:145: echo "$FSLDIR/bin/fslmaths $i -Tstd -bin ${OUTPUT}/mask_`${FSLDIR}/bin/zeropad $j 5` -odt char" >> ${LOGDIR}/drA
fsl-5.0.8/src/melodic/dual_regression:146: j=`echo "$j 1 + p" | dc -`
fsl-5.0.8/src/melodic/dual_regression-147-done
fsl-5.0.8/src/melodic/dual_regression:148:ID_drA=`$FSLDIR/bin/fsl_sub -T 10 -N drA -l $LOGDIR -t ${LOGDIR}/drA`
fsl-5.0.8/src/melodic/dual_regression-149-cat <<EOF > ${LOGDIR}/drB
fsl-5.0.8/src/melodic/dual_regression-150-#!/bin/sh
fsl-5.0.8/src/melodic/dual_regression:151:\$FSLDIR/bin/fslmerge -t ${OUTPUT}/maskALL \`\$FSLDIR/bin/imglob ${OUTPUT}/mask_*\`
fsl-5.0.8/src/melodic/dual_regression-152-\$FSLDIR/bin/fslmaths $OUTPUT/maskALL -Tmin $OUTPUT/mask
##############################################
fsl-5.0.8/src/melodic/dual_regression-155-chmod a+x ${LOGDIR}/drB
fsl-5.0.8/src/melodic/dual_regression:156:ID_drB=`$FSLDIR/bin/fsl_sub -j $ID_drA -T 5 -N drB -l $LOGDIR ${LOGDIR}/drB`
fsl-5.0.8/src/melodic/dual_regression-157-
##############################################
fsl-5.0.8/src/melodic/dual_regression-160-for i in $INPUTS ; do
fsl-5.0.8/src/melodic/dual_regression:161: s=subject`${FSLDIR}/bin/zeropad $j 5`
fsl-5.0.8/src/melodic/dual_regression-162- echo "$FSLDIR/bin/fsl_glm -i $i -d $ICA_MAPS -o $OUTPUT/dr_stage1_${s}.txt --demean -m $OUTPUT/mask ; \
##############################################
fsl-5.0.8/src/melodic/dual_regression-164- $FSLDIR/bin/fslsplit $OUTPUT/dr_stage2_$s $OUTPUT/dr_stage2_${s}_ic" >> ${LOGDIR}/drC
fsl-5.0.8/src/melodic/dual_regression:165: j=`echo "$j 1 + p" | dc -`
fsl-5.0.8/src/melodic/dual_regression-166-done
fsl-5.0.8/src/melodic/dual_regression:167:ID_drC=`$FSLDIR/bin/fsl_sub -j $ID_drB -T 30 -N drC -l $LOGDIR -t ${LOGDIR}/drC`
fsl-5.0.8/src/melodic/dual_regression-168-
##############################################
fsl-5.0.8/src/melodic/dual_regression-170-j=0
fsl-5.0.8/src/melodic/dual_regression:171:Nics=`$FSLDIR/bin/fslnvols $ICA_MAPS`
fsl-5.0.8/src/melodic/dual_regression-172-while [ $j -lt $Nics ] ; do
fsl-5.0.8/src/melodic/dual_regression:173: jj=`$FSLDIR/bin/zeropad $j 4`
fsl-5.0.8/src/melodic/dual_regression-174-
##############################################
fsl-5.0.8/src/melodic/dual_regression-183-
fsl-5.0.8/src/melodic/dual_regression:184: echo "$FSLDIR/bin/fslmerge -t $OUTPUT/dr_stage2_ic$jj \`\$FSLDIR/bin/imglob $OUTPUT/dr_stage2_subject*_ic${jj}.*\` ; \
fsl-5.0.8/src/melodic/dual_regression:185: $FSLDIR/bin/imrm \`\$FSLDIR/bin/imglob $OUTPUT/dr_stage2_subject*_ic${jj}.*\` ; $RAND" >> ${LOGDIR}/drD
fsl-5.0.8/src/melodic/dual_regression:186: j=`echo "$j 1 + p" | dc -`
fsl-5.0.8/src/melodic/dual_regression-187-done
fsl-5.0.8/src/melodic/dual_regression:188:ID_drD=`$FSLDIR/bin/fsl_sub -j $ID_drC -T 60 -N drD -l $LOGDIR -t ${LOGDIR}/drD`
fsl-5.0.8/src/melodic/dual_regression-189-
##############################################
fsl-5.0.8/src/siena/sienax-92-[ _$1 = _ ] && Usage
fsl-5.0.8/src/siena/sienax:93:Io=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/siena/sienax:94:[ `${FSLDIR}/bin/imtest ${Io}` = 0 ] && Usage
fsl-5.0.8/src/siena/sienax-95-thecommand="sienax $@"
##############################################
fsl-5.0.8/src/siena/sienax-104-stdroi=""
fsl-5.0.8/src/siena/sienax:105:origin3=37 # `fslval ${FSLDIR}/data/standard/MNI152_T1_2mm origin3`
fsl-5.0.8/src/siena/sienax:106:pixdim3=2 # `fslval ${FSLDIR}/data/standard/MNI152_T1_2mm pixdim3`
fsl-5.0.8/src/siena/sienax-107-imtype="-t 1"
##############################################
fsl-5.0.8/src/siena/sienax-132- elif [ $1 = -t ] ; then
fsl-5.0.8/src/siena/sienax:133: stdt=`echo $2 | sed 's/-/_/g'`
fsl-5.0.8/src/siena/sienax:134: stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc -`
fsl-5.0.8/src/siena/sienax-135- stdroi="$stdroi -roi 0 1000000 0 1000000 0 $stdt 0 1"
##############################################
fsl-5.0.8/src/siena/sienax-137- elif [ $1 = -b ] ; then
fsl-5.0.8/src/siena/sienax:138: stdb=`echo $2 | sed 's/-/_/g'`
fsl-5.0.8/src/siena/sienax:139: stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc -`
fsl-5.0.8/src/siena/sienax-140- stdroi="$stdroi -roi 0 1000000 0 1000000 $stdb 1000000 0 1"
##############################################
fsl-5.0.8/src/siena/sienax-178-${FSLDIR}/bin/bet $I ${I}_brain -s -m $betopts >> report.sienax
fsl-5.0.8/src/siena/sienax:179:${FSLDIR}/bin/fslmaths ${I}_brain -sub `$FSLDIR/bin/fslstats ${I}_brain -p 0` -mas ${I}_brain_mask ${I}_brain -odt float
fsl-5.0.8/src/siena/sienax:180:${FSLDIR}/bin/overlay 0 0 $I -a ${I}_brain 1 `${FSLDIR}/bin/fslstats ${I}_brain -P 95` ${I}_brain_skull 0.9 1.1 ${I}_grot
fsl-5.0.8/src/siena/sienax-181-${FSLDIR}/bin/slicer ${I}_grot -a ${I}_bet.png
##############################################
fsl-5.0.8/src/siena/sienax-189-${FSLDIR}/bin/avscale ${I}2std.mat ${FSLDIR}/data/standard/MNI152_T1_2mm > ${I}2std.avscale
fsl-5.0.8/src/siena/sienax:190:xscale=`grep Scales ${I}2std.avscale | awk '{print $4}'`
fsl-5.0.8/src/siena/sienax:191:yscale=`grep Scales ${I}2std.avscale | awk '{print $5}'`
fsl-5.0.8/src/siena/sienax:192:zscale=`grep Scales ${I}2std.avscale | awk '{print $6}'`
fsl-5.0.8/src/siena/sienax:193:vscale=`echo "10 k $xscale $yscale * $zscale * p"|dc -`
fsl-5.0.8/src/siena/sienax-194-echo "VSCALING $vscale" >> report.sienax
##############################################
fsl-5.0.8/src/siena/sienax-232- echo " volume unnormalised-volume" >> report.sienax
fsl-5.0.8/src/siena/sienax:233: S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1 -m -v`
fsl-5.0.8/src/siena/sienax:234: xa=`echo $S | awk '{print $1}'`
fsl-5.0.8/src/siena/sienax:235: xb=`echo $S | awk '{print $3}'`
fsl-5.0.8/src/siena/sienax:236: ubrain=`echo "2 k $xa $xb * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax:237: nbrain=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax-238-else
##############################################
fsl-5.0.8/src/siena/sienax-255- ${FSLDIR}/bin/fslmaths ${I}_stdmaskbrain_pve_1 -mas ${I}_stdmask_segperiph ${I}_stdmaskbrain_pve_1_segperiph -odt float
fsl-5.0.8/src/siena/sienax:256: S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1_segperiph -m -v`
fsl-5.0.8/src/siena/sienax:257: xa=`echo $S | awk '{print $1}'`
fsl-5.0.8/src/siena/sienax:258: xb=`echo $S | awk '{print $3}'`
fsl-5.0.8/src/siena/sienax:259: uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax:260: xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax-261- echo "pgrey $xg $uxg (peripheral grey)" >> report.sienax
##############################################
fsl-5.0.8/src/siena/sienax-263- ${FSLDIR}/bin/fslmaths ${I}_stdmaskbrain_pve_0 -mas ${I}_stdmask_segvent ${I}_stdmaskbrain_pve_0_segvent -odt float
fsl-5.0.8/src/siena/sienax:264: S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_0_segvent -m -v`
fsl-5.0.8/src/siena/sienax:265: xa=`echo $S | awk '{print $1}'`
fsl-5.0.8/src/siena/sienax:266: xb=`echo $S | awk '{print $3}'`
fsl-5.0.8/src/siena/sienax:267: uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax:268: xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax-269- echo "vcsf $xg $uxg (ventricular CSF)" >> report.sienax
fsl-5.0.8/src/siena/sienax-270- fi
fsl-5.0.8/src/siena/sienax:271: S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1 -m -v`
fsl-5.0.8/src/siena/sienax:272: xa=`echo $S | awk '{print $1}'`
fsl-5.0.8/src/siena/sienax:273: xb=`echo $S | awk '{print $3}'`
fsl-5.0.8/src/siena/sienax:274: ugrey=`echo "2 k $xa $xb * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax:275: ngrey=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax-276- echo "GREY $ngrey $ugrey" >> report.sienax
fsl-5.0.8/src/siena/sienax:277: S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_2 -m -v`
fsl-5.0.8/src/siena/sienax:278: xa=`echo $S | awk '{print $1}'`
fsl-5.0.8/src/siena/sienax:279: xb=`echo $S | awk '{print $3}'`
fsl-5.0.8/src/siena/sienax:280: uwhite=`echo "2 k $xa $xb * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax:281: nwhite=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax-282- echo "WHITE $nwhite $uwhite" >> report.sienax
fsl-5.0.8/src/siena/sienax-283-
fsl-5.0.8/src/siena/sienax:284: ubrain=`echo "2 k $uwhite $ugrey + 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax:285: nbrain=`echo "2 k $nwhite $ngrey + 1 / p" | dc -`
fsl-5.0.8/src/siena/sienax-286-fi
##############################################
fsl-5.0.8/src/siena/sienax-308-if [ $debug = 0 ] ; then
fsl-5.0.8/src/siena/sienax:309: /bin/rm -f `$FSLDIR/bin/imglob -extensions ${I}_brain* ${I}_stdmask*`
fsl-5.0.8/src/siena/sienax-310- /bin/rm -f ${I}2std.avscale ${I}2std_inv.mat
##############################################
fsl-5.0.8/src/siena/siena_flirt-83-[ "$2" = "" ] && Usage
fsl-5.0.8/src/siena/siena_flirt:84:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/siena/siena_flirt:85:[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
fsl-5.0.8/src/siena/siena_flirt:86:A1=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/siena/siena_flirt:87:A2=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/siena/siena_flirt-88-
##############################################
fsl-5.0.8/src/siena/siena_flirt-115-${FSLDIR}/bin/whirlgif -o ${A1}_and_${A2}.gif -time 50 -loop 0 gr${A1}${A2}j.gif gr${A1}${A2}k.gif >/dev/null 2>&1
fsl-5.0.8/src/siena/siena_flirt:116:/bin/rm gr${A1}${A2}?.??? `$FSLDIR/bin/imglob -extensions ${A2}_halfwayto_${A1}.* ${A1}_halfwayto_${A2}.*`
fsl-5.0.8/src/siena/siena_flirt-117-
##############################################
fsl-5.0.8/src/siena/siena-93-[ "$2" = "" ] && Usage
fsl-5.0.8/src/siena/siena:94:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/siena/siena:95:[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
fsl-5.0.8/src/siena/siena:96:Ao=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/siena/siena:97:Bo=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/siena/siena-98-thecommand="siena $@"
##############################################
fsl-5.0.8/src/siena/siena-109-stdroi=""
fsl-5.0.8/src/siena/siena:110:origin3=37 # `fslval ${FSLDIR}/data/standard/MNI152_T1_2mm origin3`
fsl-5.0.8/src/siena/siena:111:pixdim3=2 # `fslval ${FSLDIR}/data/standard/MNI152_T1_2mm pixdim3`
fsl-5.0.8/src/siena/siena-112-Vmask="${FSLDIR}/data/standard/MNI152_T1_2mm_VentricleMask"
##############################################
fsl-5.0.8/src/siena/siena-142- dostd=1
fsl-5.0.8/src/siena/siena:143: stdt=`echo $2 | sed 's/-/_/g'`
fsl-5.0.8/src/siena/siena:144: stdt=`echo "10 k $stdt $pixdim3 / $origin3 + p" | dc -`
fsl-5.0.8/src/siena/siena-145- stdroi="$stdroi -roi 0 1000000 0 1000000 0 $stdt 0 1"
##############################################
fsl-5.0.8/src/siena/siena-148- dostd=1
fsl-5.0.8/src/siena/siena:149: stdb=`echo $2 | sed 's/-/_/g'`
fsl-5.0.8/src/siena/siena:150: stdb=`echo "10 k $stdb $pixdim3 / $origin3 + p" | dc -`
fsl-5.0.8/src/siena/siena-151- stdroi="$stdroi -roi 0 1000000 0 1000000 $stdb 1000000 0 1"
##############################################
fsl-5.0.8/src/siena/siena-166-if [ $do_viena = yes ] ; then
fsl-5.0.8/src/siena/siena:167: if [ `${FSLDIR}/bin/imtest ${Vmask}` = 0 ] ; then
fsl-5.0.8/src/siena/siena-168- echo "ERROR:: cannot find image ${Vmask}"
##############################################
fsl-5.0.8/src/siena/siena-197-${FSLDIR}/bin/bet $B ${B}_brain -s -m $betopts >> report.siena
fsl-5.0.8/src/siena/siena:198:${FSLDIR}/bin/fslmaths ${A}_brain -sub `$FSLDIR/bin/fslstats ${A}_brain -p 0` -mas ${A}_brain_mask ${A}_brain -odt float
fsl-5.0.8/src/siena/siena:199:${FSLDIR}/bin/fslmaths ${B}_brain -sub `$FSLDIR/bin/fslstats ${B}_brain -p 0` -mas ${B}_brain_mask ${B}_brain -odt float
fsl-5.0.8/src/siena/siena:200:${FSLDIR}/bin/overlay 0 0 $A -a ${A}_brain 1 `${FSLDIR}/bin/fslstats ${A}_brain -P 95` ${A}_brain_skull 0.9 1.1 ${A}_grot
fsl-5.0.8/src/siena/siena-201-${FSLDIR}/bin/slicer ${A}_grot -a ${A}_bet.png
fsl-5.0.8/src/siena/siena:202:${FSLDIR}/bin/overlay 0 0 $B -a ${B}_brain 1 `${FSLDIR}/bin/fslstats ${B}_brain -P 95` ${B}_brain_skull 0.9 1.1 ${B}_grot
fsl-5.0.8/src/siena/siena-203-${FSLDIR}/bin/slicer ${B}_grot -a ${B}_bet.png
##############################################
fsl-5.0.8/src/siena/siena-214-echo "---------- produce valid masks --------------------------------------" >> report.siena
fsl-5.0.8/src/siena/siena:215:XDIM=`${FSLDIR}/bin/fslval $A dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
fsl-5.0.8/src/siena/siena:216:YDIM=`${FSLDIR}/bin/fslval $A dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
fsl-5.0.8/src/siena/siena:217:ZDIM=`${FSLDIR}/bin/fslval $A dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
fsl-5.0.8/src/siena/siena-218-${FSLDIR}/bin/fslmaths ${A}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${A}_valid_mask
fsl-5.0.8/src/siena/siena:219:XDIM=`${FSLDIR}/bin/fslval $B dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
fsl-5.0.8/src/siena/siena:220:YDIM=`${FSLDIR}/bin/fslval $B dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
fsl-5.0.8/src/siena/siena:221:ZDIM=`${FSLDIR}/bin/fslval $B dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
fsl-5.0.8/src/siena/siena-222-${FSLDIR}/bin/fslmaths ${B}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${B}_valid_mask
##############################################
fsl-5.0.8/src/siena/siena-239- ${FSLDIR}/bin/convert_xfm -concat ${B}_to_std_inv.mat -omat ${A}_to_${B}_tmp.mat ${A}_to_std.mat
fsl-5.0.8/src/siena/siena:240: RMSDIFF=`${FSLDIR}/bin/rmsdiff ${A}_to_${B}.mat ${A}_to_${B}_tmp.mat $A | sed 's/\..*$/ /g'` # last part makes it integer
fsl-5.0.8/src/siena/siena-241- echo "rmsdiff for standard space transform is $RMSDIFF mm" >> report.siena
##############################################
fsl-5.0.8/src/siena/siena-274-echo "---------- change analysis ------------------------------------------" >> report.siena
fsl-5.0.8/src/siena/siena:275:corr1=`${FSLDIR}/bin/siena_cal $A $B 1.002 $sdo $sdopts`
fsl-5.0.8/src/siena/siena:276:corr2=`${FSLDIR}/bin/siena_cal $B $A 1.002 $sdo $sdopts`
fsl-5.0.8/src/siena/siena:277:corr=`echo "10 k $corr1 $corr2 + 2.0 / p" | dc -`
fsl-5.0.8/src/siena/siena-278-echo "corr1=$corr1 corr2=$corr2 corr=$corr" >> report.siena
##############################################
fsl-5.0.8/src/siena/siena-281-${FSLDIR}/bin/siena_diff ${B} ${A} -c $corr $sdo $sdopts >> report.siena
fsl-5.0.8/src/siena/siena:282:pbvc_backward=`grep PBVC report.siena | tail -n 1 | awk '{print $2}' | sed 's/-/_/g'`
fsl-5.0.8/src/siena/siena-283-${FSLDIR}/bin/overlay 1 0 -c ${B}_halfwayto_${A} -a ${B}_halfwayto_${A}_brain_seg 1.1 3 ${B}_halfwayto_${A}_brain_seg_grot
##############################################
fsl-5.0.8/src/siena/siena-291-${FSLDIR}/bin/imrm ${A}_halfwayto_${B}_brain_seg_grot
fsl-5.0.8/src/siena/siena:292:pbvc_forward=`grep PBVC report.siena | tail -n 1 | awk '{print $2}' | sed 's/-/_/g'`
fsl-5.0.8/src/siena/siena-293-echo "<hr><p><b>FAST tissue segmentation</b><br>These images show the tissue segmentation used to find the brain/non-brain boundary. The exact segmentation of grey matter vs. white matter is not important.<p>${Ao}<br><IMG BORDER=0 SRC=\"${A}_halfwayto_${B}_brain_seg.png\"><p>${Bo}<br><IMG BORDER=0 SRC=\"${B}_halfwayto_${A}_brain_seg.png\">" >> report.html
##############################################
fsl-5.0.8/src/siena/siena-295-echo "" >> report.siena
fsl-5.0.8/src/siena/siena:296:pbvc_average=`echo "10 k $pbvc_forward $pbvc_backward - 2.0 / p" | dc -`
fsl-5.0.8/src/siena/siena-297-echo "finalPBVC $pbvc_average %" >> report.siena
##############################################
fsl-5.0.8/src/siena/siena_cal-82-[ "$2" = "" ] && Usage
fsl-5.0.8/src/siena/siena_cal:83:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/siena/siena_cal:84:input=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/siena/siena_cal:85:inputB=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/siena/siena_cal-86-
fsl-5.0.8/src/siena/siena_cal-87-m=$3
fsl-5.0.8/src/siena/siena_cal:88:M=`echo "5 k 1.0 $m / p" | dc -`
fsl-5.0.8/src/siena/siena_cal-89-shift 3
fsl-5.0.8/src/siena/siena_cal-90-
fsl-5.0.8/src/siena/siena_cal:91:o1=`${FSLDIR}/bin/fslval ${input} dim1`
fsl-5.0.8/src/siena/siena_cal:92:o2=`${FSLDIR}/bin/fslval ${input} dim2`
fsl-5.0.8/src/siena/siena_cal:93:o3=`${FSLDIR}/bin/fslval ${input} dim3`
fsl-5.0.8/src/siena/siena_cal-94-
fsl-5.0.8/src/siena/siena_cal:95:v1=`${FSLDIR}/bin/fslval ${input} pixdim1 | sed "s/-//g"`
fsl-5.0.8/src/siena/siena_cal:96:v2=`${FSLDIR}/bin/fslval ${input} pixdim2 | sed "s/-//g"`
fsl-5.0.8/src/siena/siena_cal:97:v3=`${FSLDIR}/bin/fslval ${input} pixdim3 | sed "s/-//g"`
fsl-5.0.8/src/siena/siena_cal-98-
fsl-5.0.8/src/siena/siena_cal:99:t1=`echo "5 k $m 1.0 - $o1 * $v1 * _0.5 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal:100:t2=`echo "5 k $m 1.0 - $o2 * $v2 * _0.5 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal:101:t3=`echo "5 k $m 1.0 - $o3 * $v3 * _0.5 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal-102-
##############################################
fsl-5.0.8/src/siena/siena_cal-107-
fsl-5.0.8/src/siena/siena_cal:108:t1=`echo "5 k $M 1.0 - $o1 * $v1 * _0.5 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal:109:t2=`echo "5 k $M 1.0 - $o2 * $v2 * _0.5 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal:110:t3=`echo "5 k $M 1.0 - $o3 * $v3 * _0.5 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal-111-
##############################################
fsl-5.0.8/src/siena/siena_cal-122-
fsl-5.0.8/src/siena/siena_cal:123:vm=`echo "10 k $m 6 ^ 1.0 - 100.0 * p" | dc -`
fsl-5.0.8/src/siena/siena_cal:124:cal=`grep PBVC ${input}_to_sc${input}.siena | awk '{print $2}' | sed "s/-//g"`
fsl-5.0.8/src/siena/siena_cal:125:corr=`echo "10 k $vm $cal / p" | dc -`
fsl-5.0.8/src/siena/siena_cal-126-
##############################################
fsl-5.0.8/src/siena/siena_flow2std-88-[ "$2" = "" ] && Usage
fsl-5.0.8/src/siena/siena_flow2std:89:[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
fsl-5.0.8/src/siena/siena_flow2std:90:[ `${FSLDIR}/bin/imtest $2` = 0 ] && Usage
fsl-5.0.8/src/siena/siena_flow2std:91:A=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/siena/siena_flow2std:92:B=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/siena/siena_flow2std-93-shift 2
##############################################
fsl-5.0.8/src/siena/siena_flow2std-110-if [ ! -f ${A}_to_std.mat ] ; then
fsl-5.0.8/src/siena/siena_flow2std:111: if [ `${FSLDIR}/bin/imtest ${A}_brain` = 0 ] ; then
fsl-5.0.8/src/siena/siena_flow2std-112- ${FSLDIR}/bin/bet $A ${A}_brain
##############################################
fsl-5.0.8/src/siena/viena_quant-47-[ "$2" = "" ] && usage
fsl-5.0.8/src/siena/viena_quant:48:[ `${FSLDIR}/bin/imtest $1` = 0 ] && usage
fsl-5.0.8/src/siena/viena_quant:49:[ `${FSLDIR}/bin/imtest $2` = 0 ] && usage
fsl-5.0.8/src/siena/viena_quant:50:[ `${FSLDIR}/bin/imtest $3` = 0 ] && usage
fsl-5.0.8/src/siena/viena_quant-51-
##############################################
fsl-5.0.8/src/siena/viena_quant-107-do
fsl-5.0.8/src/siena/viena_quant:108: if [ `${FSLDIR}/bin/imtest $VOL` = 0 ] ; then
fsl-5.0.8/src/siena/viena_quant-109- echo "Error, file does not exist: $VOL" >> $LOG
##############################################
fsl-5.0.8/src/siena/viena_quant-124-${FSLDIR}/bin/fslmaths ${scbaseflow} -mas ${scbasehalf}_ventricle_region_bin ${scbaseflow}_ventricles
fsl-5.0.8/src/siena/viena_quant:125:edgepointsbase=`${FSLDIR}/bin/fslstats ${scbaseedge}_ventricles -V | cut -d' ' -f1`
fsl-5.0.8/src/siena/viena_quant:126:infobaseflow=`${FSLDIR}/bin/fslstats ${scbaseflow}_ventricles -V -M`
fsl-5.0.8/src/siena/viena_quant:127:nonzeroflowbase=`echo ${infobaseflow} | cut -d' ' -f1`
fsl-5.0.8/src/siena/viena_quant:128:tempmeanflowbase=`echo ${infobaseflow} | cut -d' ' -f3`
fsl-5.0.8/src/siena/viena_quant:129:meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-130-
fsl-5.0.8/src/siena/viena_quant-131-# Determine only one of three pixdims because we have isotropic pixels.
fsl-5.0.8/src/siena/viena_quant:132:pixdimbase=`${FSLDIR}/bin/fslval ${scbasehalf} pixdim1`
fsl-5.0.8/src/siena/viena_quant-133-
fsl-5.0.8/src/siena/viena_quant-134-# Calculate PVVC
fsl-5.0.8/src/siena/viena_quant:135:temppvvcbase=`echo "10 k 30 ${pixdimbase} * ${meanflowbase} * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-136-
fsl-5.0.8/src/siena/viena_quant-137-# We assume standard FSL settings have been used, i.e. 0.2% change for calibration, change above if not true.
fsl-5.0.8/src/siena/viena_quant:138:vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc -`
fsl-5.0.8/src/siena/viena_quant:139:calibbase=`echo "10 k ${vm} ${temppvvcbase} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-140-
##############################################
fsl-5.0.8/src/siena/viena_quant-157-${FSLDIR}/bin/fslmaths ${scfollowflow} -mas ${scfollowhalf}_ventricle_region_bin ${scfollowflow}_ventricles
fsl-5.0.8/src/siena/viena_quant:158:edgepointsfollow=`${FSLDIR}/bin/fslstats ${scfollowedge}_ventricles -V|cut -f 1 -d " "`
fsl-5.0.8/src/siena/viena_quant:159:infofollowflow=`${FSLDIR}/bin/fslstats ${scfollowflow}_ventricles -V -M`
fsl-5.0.8/src/siena/viena_quant:160:nonzeroflowfollow=`echo ${infofollowflow} | cut -d' ' -f1`
fsl-5.0.8/src/siena/viena_quant:161:tempmeanflowfollow=`echo ${infofollowflow} | cut -d' ' -f3`
fsl-5.0.8/src/siena/viena_quant:162:meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-163-
fsl-5.0.8/src/siena/viena_quant-164-# Determine only one of three pixdims because we have isotropic pixels.
fsl-5.0.8/src/siena/viena_quant:165:pixdimfollow=`${FSLDIR}/bin/fslval ${scfollowhalf} pixdim1`
fsl-5.0.8/src/siena/viena_quant-166-
fsl-5.0.8/src/siena/viena_quant-167-# Calculate PVVC
fsl-5.0.8/src/siena/viena_quant:168:temppvvcfollow=`echo "10 k 30 ${pixdimfollow} * ${meanflowfollow} * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-169-
fsl-5.0.8/src/siena/viena_quant-170-# We assume standard FSL settings have been used, i.e. 0.2% change for calibration, change above if not true.
fsl-5.0.8/src/siena/viena_quant:171:vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc -`
fsl-5.0.8/src/siena/viena_quant:172:calibfollow=`echo "10 k ${vm} ${temppvvcfollow} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-173-
##############################################
fsl-5.0.8/src/siena/viena_quant-205-
fsl-5.0.8/src/siena/viena_quant:206:edgepointsbase=`${FSLDIR}/bin/fslstats ${base}_to_${follow}_edgepoints_ventricles -V|cut -f 1 -d " "`
fsl-5.0.8/src/siena/viena_quant:207:infobaseflow=`${FSLDIR}/bin/fslstats ${base}_to_${follow}_flow_ventricles -V -M`
fsl-5.0.8/src/siena/viena_quant:208:nonzeroflowbase=`echo ${infobaseflow}|cut -f 1 -d " "`
fsl-5.0.8/src/siena/viena_quant:209:tempmeanflowbase=`echo ${infobaseflow}|cut -f 3 -d " "`
fsl-5.0.8/src/siena/viena_quant:210:meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant:211:pixdimbase=`${FSLDIR}/bin/fslval ${base}_halfwayto_${follow} pixdim1`
fsl-5.0.8/src/siena/viena_quant-212-
fsl-5.0.8/src/siena/viena_quant:213:edgepointsfollow=`${FSLDIR}/bin/fslstats ${follow}_to_${base}_edgepoints_ventricles -V|cut -f 1 -d " "`
fsl-5.0.8/src/siena/viena_quant:214:infofollowflow=`${FSLDIR}/bin/fslstats ${follow}_to_${base}_flow_ventricles -V -M`
fsl-5.0.8/src/siena/viena_quant:215:nonzeroflowfollow=`echo ${infofollowflow} | cut -f 1 -d " "`
fsl-5.0.8/src/siena/viena_quant:216:tempmeanflowfollow=`echo ${infofollowflow} | cut -f 3 -d " "`
fsl-5.0.8/src/siena/viena_quant:217:meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant:218:pixdimfollow=`${FSLDIR}/bin/fslval ${follow}_halfwayto_${base} pixdim1`
fsl-5.0.8/src/siena/viena_quant-219-
fsl-5.0.8/src/siena/viena_quant-220-# Calculate PVVC base -> follow
fsl-5.0.8/src/siena/viena_quant:221:pvvcbasetofollow=`echo "10 k 30 ${calibbase} * ${pixdimbase} * ${meanflowbase} * _1.0 * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-222-
fsl-5.0.8/src/siena/viena_quant-223-# Calculate PVVC follow -> base
fsl-5.0.8/src/siena/viena_quant:224:pvvcfollowtobase=`echo "10 k 30 ${calibfollow} * ${pixdimfollow} * ${meanflowfollow} * _1.0 * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant:225:denom=`echo "10 k ${pvvcfollowtobase} 100 / 1.0 + p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant:226:tmpbackwards=`echo "10 k ${pvvcfollowtobase} ${denom} / _1.0 * p" |sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-227-
fsl-5.0.8/src/siena/viena_quant:228:meanpvvc=`echo "10 k ${pvvcbasetofollow} ${tmpbackwards} + 2 / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/src/siena/viena_quant-229-
##############################################
fsl-5.0.8/src/fabber/fabber_var-88-if [ -z $paramflag ]; then
fsl-5.0.8/src/fabber/fabber_var:89: params=`cat $datdir/paramnames.txt`
fsl-5.0.8/src/fabber/fabber_var-90-else
fsl-5.0.8/src/fabber/fabber_var:91: params=`echo $params | sed 's:,: :g'`
fsl-5.0.8/src/fabber/fabber_var-92-fi
##############################################
fsl-5.0.8/src/fabber/fabber_var-95-for param in $params; do
fsl-5.0.8/src/fabber/fabber_var:96: index=`grep -n $param $datdir/paramnames.txt | sed -n 's/^\([0-9]*\)[:].*/\1/p'`
fsl-5.0.8/src/fabber/fabber_var-97- if [ -z $index ];then
##############################################
fsl-5.0.8/src/fabber/fabber_var-102- fi
fsl-5.0.8/src/fabber/fabber_var:103: #index=`echo "$index +1" | bc`
fsl-5.0.8/src/fabber/fabber_var-104-done
##############################################
fsl-5.0.8/src/avwutils/fslreorient2std-73-if [ $# -lt 1 ] ; then
fsl-5.0.8/src/avwutils/fslreorient2std:74: echo "Usage: `basename $0` <input_image> [output_image]"
fsl-5.0.8/src/avwutils/fslreorient2std-75- echo " "
fsl-5.0.8/src/avwutils/fslreorient2std:76: echo "`basename $0` is a tool for reorienting the image to match the"
fsl-5.0.8/src/avwutils/fslreorient2std-77- echo "approximate orientation of the standard template images (MNI152)."
##############################################
fsl-5.0.8/src/avwutils/fslreorient2std-88-
fsl-5.0.8/src/avwutils/fslreorient2std:89:img=`$FSLDIR/bin/remove_ext $1`;
fsl-5.0.8/src/avwutils/fslreorient2std-90-outimg=$2;
fsl-5.0.8/src/avwutils/fslreorient2std-91-
fsl-5.0.8/src/avwutils/fslreorient2std:92:if [ `$FSLDIR/bin/imtest $img` = 0 ] ; then
fsl-5.0.8/src/avwutils/fslreorient2std-93- echo "ERROR: Could not find image $1" 1>&2
##############################################
fsl-5.0.8/src/avwutils/fslreorient2std-96-
fsl-5.0.8/src/avwutils/fslreorient2std:97:scode=`$FSLDIR/bin/fslval $img sform_code`;
fsl-5.0.8/src/avwutils/fslreorient2std:98:qcode=`$FSLDIR/bin/fslval $img qform_code`;
fsl-5.0.8/src/avwutils/fslreorient2std-99-if [ $scode = 0 -a $qcode = 0 ] ; then
##############################################
fsl-5.0.8/src/avwutils/fslreorient2std-111-$FSLDIR/bin/fslhd $img | grep $pattern | awk '{ print $2 " " $3 " " $4 " " $5 }' > ${outimg}_nii.mat
fsl-5.0.8/src/avwutils/fslreorient2std:112:det=`$FSLDIR/bin/avscale ${outimg}_nii.mat | grep Determinant | awk '{ print $3 }'`;
fsl-5.0.8/src/avwutils/fslreorient2std:113:if [ X`echo "if ( $det < 0 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/avwutils/fslreorient2std-114- # radiological case (negative determinant)
##############################################
fsl-5.0.8/src/avwutils/fsledithd-93-
fsl-5.0.8/src/avwutils/fsledithd:94:tmpbase=`${FSLDIR}/bin/tmpnam`;
fsl-5.0.8/src/avwutils/fsledithd:95:tmpbase2=`${FSLDIR}/bin/tmpnam`;
fsl-5.0.8/src/avwutils/fsledithd-96-
##############################################
fsl-5.0.8/src/avwutils/fsledithd-110-# exit if the above didn't generate a decent file
fsl-5.0.8/src/avwutils/fsledithd:111:if [ `cat ${tmpbase} | wc -l` -le 1 ] ; then
fsl-5.0.8/src/avwutils/fsledithd-112- exit 0;
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-80- pre="";
fsl-5.0.8/src/avwutils/fslswapdim:81: k2=`echo $1 | tr RLAPSI LRPAIS`;
fsl-5.0.8/src/avwutils/fslswapdim-82- for fn in "$2:x" "$3:y" "$4:z" ; do
fsl-5.0.8/src/avwutils/fslswapdim:83: ff=`echo $fn | sed 's/:.*//'`;
fsl-5.0.8/src/avwutils/fslswapdim:84: aa=`echo $fn | sed 's/.*://'`;
fsl-5.0.8/src/avwutils/fslswapdim-85- if [ $ff = $1 ] ; then ax=$aa ; fi
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-105-
fsl-5.0.8/src/avwutils/fslswapdim:106:filetype=`$FSLDIR/bin/fslval $1 file_type`;
fsl-5.0.8/src/avwutils/fslswapdim-107-if [ $filetype = "ANALYZE-7.5" ] ; then
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-114-if [ $nifti = yes ] ; then
fsl-5.0.8/src/avwutils/fslswapdim:115: if [ `$FSLDIR/bin/fslval $1 sform_code` -gt 0 ] ; then
fsl-5.0.8/src/avwutils/fslswapdim:116: labs=`$FSLDIR/bin/fslhd $1 | grep sform_.orient | sed 's/[^A-Z]//g'`;
fsl-5.0.8/src/avwutils/fslswapdim:117: elif [ `$FSLDIR/bin/fslval $1 qform_code` -gt 0 ] ; then
fsl-5.0.8/src/avwutils/fslswapdim:118: labs=`$FSLDIR/bin/fslhd $1 | grep qform_.orient | sed 's/[^A-Z]//g'`;
fsl-5.0.8/src/avwutils/fslswapdim-119- else
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-130-for fn in $2 $3 $4 ; do
fsl-5.0.8/src/avwutils/fslswapdim:131: cc=`echo Q$fn | sed 's/[RLAPIS]//g'`;
fsl-5.0.8/src/avwutils/fslswapdim-132- if [ $cc = "Q" ] ; then
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-141- fi
fsl-5.0.8/src/avwutils/fslswapdim:142: cc=`get_axis $fn $labs`;
fsl-5.0.8/src/avwutils/fslswapdim-143- else
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-152- if [ X$5 != X ] ; then
fsl-5.0.8/src/avwutils/fslswapdim:153: if [ `$FSLDIR/bin/remove_ext $1` != `$FSLDIR/bin/remove_ext $5` ] ; then
fsl-5.0.8/src/avwutils/fslswapdim-154- comm="$FSLDIR/bin/imcp $1 $5"
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-167- # the line below just checks the swapping syntax - it does not require the true image, as any will do since the arguments are now reduced to x/y/z format
fsl-5.0.8/src/avwutils/fslswapdim:168: check="`$FSLDIR/bin/fslswapdim_exe $FSLDIR/data/standard/MNI152_T1_2mm_brain $comm2 --checkLR`"
fsl-5.0.8/src/avwutils/fslswapdim:169: wl=`echo $check | grep -i changed | wc -l`;
fsl-5.0.8/src/avwutils/fslswapdim-170- if [ $wl -gt 0 ] ; then
##############################################
fsl-5.0.8/src/avwutils/fslswapdim-172- echo "Try the following command instead:"
fsl-5.0.8/src/avwutils/fslswapdim:173: arg234=`echo "$2 $3 $4" | sed 's/RL/LRXX/g' | sed 's/LR/RL/g' | sed 's/RLXX/LR/g' | sed 's/-x/XX-x/g' | sed 's/ x / -x /g' | sed 's/XX-x/x/g'`;
fsl-5.0.8/src/avwutils/fslswapdim-174- echo "fslswapdim $1 $arg234 $5"
##############################################
fsl-5.0.8/src/avwutils/fslanimate-77-
fsl-5.0.8/src/avwutils/fslanimate:78:im=`${FSLDIR}/bin/remove_ext $1`; export im;
fsl-5.0.8/src/avwutils/fslanimate:79:im=`basename $im`; export im;
fsl-5.0.8/src/avwutils/fslanimate:80:iout=`basename $2 .gif`; export iout;
fsl-5.0.8/src/avwutils/fslanimate-81-
##############################################
fsl-5.0.8/src/avwutils/fslanimate-89-cwd=`pwd`; export cwd
fsl-5.0.8/src/avwutils/fslanimate:90:imdir=`dirname $1 | sed 's/^\.\./.\/../'`; export imdir
fsl-5.0.8/src/avwutils/fslanimate:91:if [ "X"`echo $imdir | grep '^\.'`"X" != "XX" ] ; then
fsl-5.0.8/src/avwutils/fslanimate-92- imdir="$cwd/$imdir"; export imdir;
fsl-5.0.8/src/avwutils/fslanimate-93-fi
fsl-5.0.8/src/avwutils/fslanimate:94:imoutdir=`dirname $2 | sed 's/^\.\./.\/../'`; export imoutdir;
fsl-5.0.8/src/avwutils/fslanimate:95:if [ "X"`echo $imoutdir | grep '^\.'`"X" != "XX" ] ; then
fsl-5.0.8/src/avwutils/fslanimate-96- imoutdir="$cwd/$imoutdir"; export imoutdir;
##############################################
fsl-5.0.8/src/avwutils/fslanimate-106-
fsl-5.0.8/src/avwutils/fslanimate:107:ntime=`$FSLDIR/bin/fslval $imdir/$im dim4`; export ntime;
fsl-5.0.8/src/avwutils/fslanimate-108-if [ $ntime -le 1 ] ; then
##############################################
fsl-5.0.8/src/avwutils/fslanimate-116-$FSLDIR/bin/fslsplit $im
fsl-5.0.8/src/avwutils/fslanimate:117:for fnm in `$FSLDIR/bin/imglob vol*` ; do
fsl-5.0.8/src/avwutils/fslanimate:118: num=`echo $fnm | sed 's/vol//'`; export num;
fsl-5.0.8/src/avwutils/fslanimate-119- echo $num;
##############################################
fsl-5.0.8/src/avwutils/fslchfiletype-82-
fsl-5.0.8/src/avwutils/fslchfiletype:83:oldfile=`$FSLDIR/bin/remove_ext $2`
fsl-5.0.8/src/avwutils/fslchfiletype-84-
fsl-5.0.8/src/avwutils/fslchfiletype-85-if [ $# -ge 3 ] ; then
fsl-5.0.8/src/avwutils/fslchfiletype:86: newfile=`$FSLDIR/bin/remove_ext $3`
fsl-5.0.8/src/avwutils/fslchfiletype-87- inplace=0
fsl-5.0.8/src/avwutils/fslchfiletype-88-else
fsl-5.0.8/src/avwutils/fslchfiletype:89: newfile=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/avwutils/fslchfiletype-90- inplace=1
##############################################
fsl-5.0.8/src/avwutils/fslchfiletype-98-if [ $inplace = 1 ] ; then
fsl-5.0.8/src/avwutils/fslchfiletype:99: if [ `$FSLDIR/bin/imtest $newfile` = 1 ] ; then
fsl-5.0.8/src/avwutils/fslchfiletype-100- $FSLDIR/bin/immv $newfile ${oldfile}TMP
fsl-5.0.8/src/avwutils/fslchfiletype:101: if [ `$FSLDIR/bin/imtest ${oldfile}TMP` = 1 ] ; then
fsl-5.0.8/src/avwutils/fslchfiletype-102- $FSLDIR/bin/imrm $oldfile
##############################################
fsl-5.0.8/src/avwutils/test_write.sh-74-for fn in ANALYZE:1 NIFTI_PAIR:2 NIFTI:3 ANALYZE_GZ:4 NIFTI_PAIR_GZ:5 NIFTI_GZ:6 ; do
fsl-5.0.8/src/avwutils/test_write.sh:75: num=`echo $fn | sed 's/.*://'`;
fsl-5.0.8/src/avwutils/test_write.sh:76: opt=`echo $fn | sed 's/:.*//'`;
fsl-5.0.8/src/avwutils/test_write.sh-77- export FSLOUTPUTTYPE=$opt
##############################################
fsl-5.0.8/src/avwutils/test_write.sh-85-for fn in epimj[1-6].* episs[1-6].* ; do
fsl-5.0.8/src/avwutils/test_write.sh:86: val=`../niftiio/nifti1_test $fn | grep nifti_type`;
fsl-5.0.8/src/avwutils/test_write.sh-87- echo " XXXXX $fn XXXXX $val "
##############################################
fsl-5.0.8/src/avwutils/fslsize-72-if [ $# -lt 1 ] ; then
fsl-5.0.8/src/avwutils/fslsize:73: echo "Usage: `basename $0` <filename> [-s]" ;
fsl-5.0.8/src/avwutils/fslsize-74- echo " -s output using short format (one line)"
##############################################
fsl-5.0.8/src/avwutils/fslsize-85-else
fsl-5.0.8/src/avwutils/fslsize:86: sz=`$FSLDIR/bin/fslhd $1 | cat -v | grep dim[1-4] | sed 's/pixdim4.*//' | sed 's/pixdim1/ : Dims = /' | sed 's/^dim1/Size = /' | sed 's/[pix]*dim.[ ]*/ x /'`;
fsl-5.0.8/src/avwutils/fslsize-87- echo $sz
##############################################
fsl-5.0.8/src/avwutils/fslmodhd-75- echo ""
fsl-5.0.8/src/avwutils/fslmodhd:76: echo "Usage: `basename $0` <image> <keyword> <value>"
fsl-5.0.8/src/avwutils/fslmodhd-77- echo ""
##############################################
fsl-5.0.8/src/avwutils/fslmodhd-103-
fsl-5.0.8/src/avwutils/fslmodhd:104:tmpbase=`${FSLDIR}/bin/tmpnam`;
fsl-5.0.8/src/avwutils/fslmodhd-105-
##############################################
fsl-5.0.8/src/avwutils/fslmodhd-108-# exit if the above didn't generate a decent file
fsl-5.0.8/src/avwutils/fslmodhd:109:if [ `cat ${tmpbase} | wc -l` -le 1 ] ; then
fsl-5.0.8/src/avwutils/fslmodhd-110- exit 0;
##############################################
fsl-5.0.8/src/avwutils/fslmodhd-113-# modify header, reprocess and pass onto fslcreatehd
fsl-5.0.8/src/avwutils/fslmodhd:114:if [ `cat ${tmpbase} | grep "^[ ]*$keyword[ ]*=[ ]*" | wc -l` = 0 ] ; then
fsl-5.0.8/src/avwutils/fslmodhd-115- # this keyword is not in the fslhd output so add it
##############################################
fsl-5.0.8/src/avwutils/sliceanimate-76-
fsl-5.0.8/src/avwutils/sliceanimate:77:volname=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/avwutils/sliceanimate:78:bnm=`basename $volname`;
fsl-5.0.8/src/avwutils/sliceanimate-79-shift
fsl-5.0.8/src/avwutils/sliceanimate-80-
fsl-5.0.8/src/avwutils/sliceanimate:81:nn=`$FSLDIR/bin/fslval $volname dim3`;
fsl-5.0.8/src/avwutils/sliceanimate-82-n=0;
fsl-5.0.8/src/avwutils/sliceanimate-83-
fsl-5.0.8/src/avwutils/sliceanimate:84:tmpnam=`basename ${volname}`_TMP
fsl-5.0.8/src/avwutils/sliceanimate-85-tmpdir=/tmp
##############################################
fsl-5.0.8/src/avwutils/sliceanimate-89- $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}.png
fsl-5.0.8/src/avwutils/sliceanimate:90: snum=`echo "0000${n}" | sed 's/^.*\(....\)$/\1/'`;
fsl-5.0.8/src/avwutils/sliceanimate-91- echo slice $snum
fsl-5.0.8/src/avwutils/sliceanimate-92- ${FSLDIR}/bin/pngappend $tmpdir/${tmpnam}.png $tmpdir/${bnm}_slice${snum}.gif
fsl-5.0.8/src/avwutils/sliceanimate:93: n=`echo $n + 1 | bc`;
fsl-5.0.8/src/avwutils/sliceanimate-94-done
##############################################
fsl-5.0.8/src/avwutils/fslcorrecthd.cc-146-
fsl-5.0.8/src/avwutils/fslcorrecthd.cc:147: system(("FSLOUTPUTTYPE=NIFTI; ${FSLDIR}/bin/fslmaths " + string(outputName)).c_str()); //To clean up header
fsl-5.0.8/src/avwutils/fslcorrecthd.cc-148- free(temp);
##############################################
fsl-5.0.8/src/avwutils/fslchpixdim-77-
fsl-5.0.8/src/avwutils/fslchpixdim:78:if [ `${FSLDIR}/bin/imtest $1` = 0 ] ; then
fsl-5.0.8/src/avwutils/fslchpixdim-79- echo "Cannot find image $1";
##############################################
fsl-5.0.8/src/avwutils/fslchpixdim-82-
fsl-5.0.8/src/avwutils/fslchpixdim:83:xsz=`$FSLDIR/bin/fslval $1 dim1`;
fsl-5.0.8/src/avwutils/fslchpixdim:84:ysz=`$FSLDIR/bin/fslval $1 dim2`;
fsl-5.0.8/src/avwutils/fslchpixdim:85:zsz=`$FSLDIR/bin/fslval $1 dim3`;
fsl-5.0.8/src/avwutils/fslchpixdim:86:tsz=`$FSLDIR/bin/fslval $1 dim4`;
fsl-5.0.8/src/avwutils/fslchpixdim:87:dt=`$FSLDIR/bin/fslval $1 datatype`;
fsl-5.0.8/src/avwutils/fslchpixdim:88:xor=`$FSLDIR/bin/fslval $1 origin1`;
fsl-5.0.8/src/avwutils/fslchpixdim:89:yor=`$FSLDIR/bin/fslval $1 origin2`;
fsl-5.0.8/src/avwutils/fslchpixdim:90:zor=`$FSLDIR/bin/fslval $1 origin3`;
fsl-5.0.8/src/avwutils/fslchpixdim:91:tr=`$FSLDIR/bin/fslval $1 pixdim4`;
fsl-5.0.8/src/avwutils/fslchpixdim-92-
##############################################
fsl-5.0.8/src/avwutils/fslchpixdim-105-
fsl-5.0.8/src/avwutils/fslchpixdim:106:flag=`$FSLDIR/bin/fslhd $1 | cat -v | grep swapping | wc -w`;
fsl-5.0.8/src/avwutils/fslchpixdim-107-if [ $flag -eq 0 ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-90- for p in avw2afni avw2ascii avwanimate avwcc avwcheck avwchfiletype avwchpixdim avwcomplex avwconv avwcpgeom avwcreatehd avwedithd avwfft avwfill avwhd avwinfo avwinterleave avwmaths avwmeants avwmerge avwnvols avworient avwpspec avwroi avwsize avwslice avwsplit avwstats avwswapdim avwval ; do
fsl-5.0.8/src/avwutils/avw2fsl:91: q=`echo $p | sed 's/avw/fsl/g'`
fsl-5.0.8/src/avwutils/avw2fsl-92- sed "s/${p}/${q}/g" $s > ${s}_tmp ; /bin/mv ${s}_tmp $s
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-100- # warn about "ip"
fsl-5.0.8/src/avwutils/avw2fsl:101: w=`cat $s | grep "ip "`
fsl-5.0.8/src/avwutils/avw2fsl-102- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-108- # warn about "-ero2"
fsl-5.0.8/src/avwutils/avw2fsl:109: w=`cat $s | grep fslmaths | grep " -ero2 "`
fsl-5.0.8/src/avwutils/avw2fsl-110- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-115- # warn about "-dil2"
fsl-5.0.8/src/avwutils/avw2fsl:116: w=`cat $s | grep fslmaths | grep " -dil2 "`
fsl-5.0.8/src/avwutils/avw2fsl-117- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-122- # warn about "-dil"
fsl-5.0.8/src/avwutils/avw2fsl:123: w=`cat $s | grep fslmaths | grep " -dil "`
fsl-5.0.8/src/avwutils/avw2fsl-124- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-129- # warn about "susan_smooth"
fsl-5.0.8/src/avwutils/avw2fsl:130: w=`cat $s | grep susan_smooth`
fsl-5.0.8/src/avwutils/avw2fsl-131- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-137- for p in fsl2ascii fslcc fslinterleave fslmaths fslroi bet ; do
fsl-5.0.8/src/avwutils/avw2fsl:138: w=`cat $s | grep ${p}_8UI`
fsl-5.0.8/src/avwutils/avw2fsl-139- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-142- fi
fsl-5.0.8/src/avwutils/avw2fsl:143: w=`cat $s | grep ${p}_16SI`
fsl-5.0.8/src/avwutils/avw2fsl-144- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-147- fi
fsl-5.0.8/src/avwutils/avw2fsl:148: w=`cat $s | grep ${p}_32SI`
fsl-5.0.8/src/avwutils/avw2fsl-149- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-152- fi
fsl-5.0.8/src/avwutils/avw2fsl:153: w=`cat $s | grep ${p}_32R`
fsl-5.0.8/src/avwutils/avw2fsl-154- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/avwutils/avw2fsl-157- fi
fsl-5.0.8/src/avwutils/avw2fsl:158: w=`cat $s | grep ${p}_64R`
fsl-5.0.8/src/avwutils/avw2fsl-159- if [ "$w" != "" ] ; then
##############################################
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-113- foreach option $lopt {
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl:114: set include($option) 1
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-115- }
##############################################
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-143- set option [lindex $optdesc 0]
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl:144: if { (![info exists include] || [info exists include($option)]) &&
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-145- ![info exists remove($option)] } {
##############################################
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-220- foreach option $lopt {
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl:221: set include($option) 1
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-222- }
##############################################
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-251- set subOption $option
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl:252: if { (![info exists include] || [info exists include($option)]) &&
fsl-5.0.8/src/misc_tcl/BWidget/widget.tcl-253- ![info exists remove($option)] } {
##############################################
fsl-5.0.8/src/misc_scripts/Text2Vest-66-if [ $# -lt 2 ] ; then
fsl-5.0.8/src/misc_scripts/Text2Vest:67: echo "`basename $0` <text file> <vest file>"
fsl-5.0.8/src/misc_scripts/Text2Vest-68- exit 0
##############################################
fsl-5.0.8/src/misc_scripts/Text2Vest-70-
fsl-5.0.8/src/misc_scripts/Text2Vest:71:NumPoints=`wc $1 | awk '{ print $1 }'`
fsl-5.0.8/src/misc_scripts/Text2Vest:72:NumWaves=`wc $1 | awk '{ print $2 }'`
fsl-5.0.8/src/misc_scripts/Text2Vest:73:NumWaves=`expr $NumWaves / $NumPoints`
fsl-5.0.8/src/misc_scripts/Text2Vest-74-
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-14- echo ""
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:15: echo "Usage: `basename $0` [options] <image1> ... <imageN>"
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-16- echo ""
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-28- echo ""
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:29: echo "e.g.: `basename $0` -n -o output_name im1 im2"
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-30- echo " Note that N>=2 (i.e. there must be at least two images in the list)"
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-60- -o)
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:61: output=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-62- shift 2;;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-63- -s)
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:64: StandardImage=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-65- shift 2;;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-66- -m)
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:67: StandardMask=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-68- shift 2;;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-69- -w)
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:70: wdir=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-71- cleanup=no;
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-73- -b)
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:74: BrainSizeOpt=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-75- BrainSizeOpt="-b $BrainSizeOpt";
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-86- *)
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:87: if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-88- echo "Unrecognised option $1" 1>&2
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-101-
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:102:if [ `echo $imagelist | wc -w` -lt 2 ] ; then
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-103- Usage;
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-110-if [ X$wdir = X ] ; then
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:111: wdir=`$FSLDIR/bin/tmpnam`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-112- wdir=${wdir}_wdir
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-124-for fn in $imagelist ; do
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:125: bnm=`$FSLDIR/bin/remove_ext $fn`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:126: bnm=`basename $bnm`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:127: fullpathfn=`$FSLDIR/bin/fsl_abspath $fn`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-128- $FSLDIR/bin/imcp $fullpathfn $wdir/$bnm
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-143-# register images together, using standard space brain masks
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:144:im1=`echo $newimlist | awk '{ print $1 }'`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-145-for im2 in $newimlist ; do
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-167-for fn in $newimlist ; do
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:168: num=`$FSLDIR/bin/zeropad $n 4`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:169: n=`echo $n + 1 | bc`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-170- if [ $crop = yes ] ; then
##############################################
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-178-# average outputs
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:179:comm=`echo ${wdir}/ImToHalf* | sed "s@ ${wdir}/ImToHalf@ -add ${wdir}/ImToHalf@g"`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage:180:tot=`echo ${wdir}/ImToHalf* | wc -w`;
fsl-5.0.8/src/misc_scripts/AnatomicalAverage-181-$FSLDIR/bin/fslmaths ${comm} -div $tot ${output}
##############################################
fsl-5.0.8/src/misc_scripts/fslFixText-3-if [ $# -ne 2 ] ; then
fsl-5.0.8/src/misc_scripts/fslFixText:4: echo "Usage: `basename $0` <input text file> <output text file>"
fsl-5.0.8/src/misc_scripts/fslFixText-5- echo "Ensures standard UNIX line endings in output text file"
##############################################
fsl-5.0.8/src/misc_scripts/fslFixText-13- # make a temporary to avoid the original being wiped
fsl-5.0.8/src/misc_scripts/fslFixText:14: tmpfile=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/misc_scripts/fslFixText-15- cp $file $tmpfile
##############################################
fsl-5.0.8/src/misc_scripts/fslFixText-19-
fsl-5.0.8/src/misc_scripts/fslFixText:20:ftype=`printf "FsLRaNdOmfSlrAnDOMFsLRaNdOmfSlrAnDOMFsLRaNdOmfSlrAnDOMFsLRaNdOm" | cat - $file | file -`
fsl-5.0.8/src/misc_scripts/fslFixText:21:if [ `echo "$ftype" | grep -i "ascii text" | wc -w` -gt 0 ] ; then
fsl-5.0.8/src/misc_scripts/fslFixText:22: if [ `echo "$ftype" | grep -i "CRLF line terminators" | wc -w` -gt 0 ] ; then
fsl-5.0.8/src/misc_scripts/fslFixText-23- cat $file | tr -d '\r' > $outfile
fsl-5.0.8/src/misc_scripts/fslFixText:24: elif [ `echo "$ftype" | grep -i "CR line terminators" | wc -w` -gt 0 ] ; then
fsl-5.0.8/src/misc_scripts/fslFixText-25- cat $file | tr '\r' '\n' > $outfile
##############################################
fsl-5.0.8/src/misc_scripts/Vest2Text-66-if [ $# -lt 2 ] ; then
fsl-5.0.8/src/misc_scripts/Vest2Text:67: echo "`basename $0` <vest file> <text file>"
fsl-5.0.8/src/misc_scripts/Vest2Text-68- exit 0
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-79-Usage() {
fsl-5.0.8/src/misc_scripts/fsl_anat:80: echo "Usage: `basename $0` [options] -i <structural image>"
fsl-5.0.8/src/misc_scripts/fsl_anat:81: echo " `basename $0` [options] -d <existing anat directory>"
fsl-5.0.8/src/misc_scripts/fsl_anat:82: #echo " `basename $0` [options] --list=<list of image names OR a text file>"
fsl-5.0.8/src/misc_scripts/fsl_anat-83- echo " "
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-110-get_opt1() {
fsl-5.0.8/src/misc_scripts/fsl_anat:111: arg=`echo $1 | sed 's/=.*//'`
fsl-5.0.8/src/misc_scripts/fsl_anat-112- echo $arg
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-116-get_arg1() {
fsl-5.0.8/src/misc_scripts/fsl_anat:117: if [ X`echo $1 | grep '='` = X ] ; then
fsl-5.0.8/src/misc_scripts/fsl_anat-118- echo "Option $1 requires an argument" 1>&2
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-120- else
fsl-5.0.8/src/misc_scripts/fsl_anat:121: arg=`echo $1 | sed 's/.*=//'`
fsl-5.0.8/src/misc_scripts/fsl_anat-122- if [ X$arg = X ] ; then
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-131-get_imarg1() {
fsl-5.0.8/src/misc_scripts/fsl_anat:132: arg=`get_arg1 $1`;
fsl-5.0.8/src/misc_scripts/fsl_anat:133: arg=`$FSLDIR/bin/remove_ext $arg`;
fsl-5.0.8/src/misc_scripts/fsl_anat-134- echo $arg
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-147-get_imarg2() {
fsl-5.0.8/src/misc_scripts/fsl_anat:148: arg=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat:149: arg=`$FSLDIR/bin/remove_ext $arg`;
fsl-5.0.8/src/misc_scripts/fsl_anat-150- echo $arg
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-203-while [ $# -ge 1 ] ; do
fsl-5.0.8/src/misc_scripts/fsl_anat:204: iarg=`get_opt1 $1`;
fsl-5.0.8/src/misc_scripts/fsl_anat-205- case "$iarg"
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-207- -i)
fsl-5.0.8/src/misc_scripts/fsl_anat:208: inputimage=`get_imarg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat-209- shift 2;;
fsl-5.0.8/src/misc_scripts/fsl_anat-210- -o)
fsl-5.0.8/src/misc_scripts/fsl_anat:211: outputname=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat-212- shift 2;;
fsl-5.0.8/src/misc_scripts/fsl_anat-213- -d)
fsl-5.0.8/src/misc_scripts/fsl_anat:214: anatdir=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat-215- shift 2;;
fsl-5.0.8/src/misc_scripts/fsl_anat-216- -s)
fsl-5.0.8/src/misc_scripts/fsl_anat:217: smooth=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat-218- shift 2;;
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-220- use_lesionmask=yes;
fsl-5.0.8/src/misc_scripts/fsl_anat:221: lesionmask=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat-222- shift 2;;
fsl-5.0.8/src/misc_scripts/fsl_anat-223- -t)
fsl-5.0.8/src/misc_scripts/fsl_anat:224: typestr=`get_arg2 $1 $2`;
fsl-5.0.8/src/misc_scripts/fsl_anat-225- if [ $typestr = T1 ] ; then type=1; fi
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-229- --list)
fsl-5.0.8/src/misc_scripts/fsl_anat:230: imagelist=`get_arg1 $1`;
fsl-5.0.8/src/misc_scripts/fsl_anat-231- multipleimages=yes;
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-268- --betfparam)
fsl-5.0.8/src/misc_scripts/fsl_anat:269: betfparam=`get_arg1 $1`;
fsl-5.0.8/src/misc_scripts/fsl_anat-270- shift;;
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-280- *)
fsl-5.0.8/src/misc_scripts/fsl_anat:281: #if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then
fsl-5.0.8/src/misc_scripts/fsl_anat-282- echo "Unrecognised option $1" 1>&2
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-340- fi
fsl-5.0.8/src/misc_scripts/fsl_anat:341: outputname=`$FSLDIR/bin/fsl_abspath $anatdir`;
fsl-5.0.8/src/misc_scripts/fsl_anat:342: outputname=`echo $outputname | sed 's/\.anat$//'`;
fsl-5.0.8/src/misc_scripts/fsl_anat-343- if [ ! -d ${outputname}.anat ] ; then
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-358- fi
fsl-5.0.8/src/misc_scripts/fsl_anat:359: im1=`echo $imagelist | sed 's/,/ /g' | awk '{ print $1 }'`;
fsl-5.0.8/src/misc_scripts/fsl_anat-360- if [ $FSLDIR/bin/imtest $im1 = 1 ] ; then
fsl-5.0.8/src/misc_scripts/fsl_anat-361- # this is a comma separated list of image names
fsl-5.0.8/src/misc_scripts/fsl_anat:362: namelist="`echo ${imagelist} | sed 's/,/ /g'`";
fsl-5.0.8/src/misc_scripts/fsl_anat-363- else
fsl-5.0.8/src/misc_scripts/fsl_anat-364- # this is a file containing the image names
fsl-5.0.8/src/misc_scripts/fsl_anat:365: namelist="`cat ${imagelist}`";
fsl-5.0.8/src/misc_scripts/fsl_anat-366- fi
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-397- mkdir average_dir
fsl-5.0.8/src/misc_scripts/fsl_anat:398: run $FSLDIR/bin/AnatomicalAverage -w average_dir -o ${T1} `$FSLDIR/bin/imglob ${T1}_*`
fsl-5.0.8/src/misc_scripts/fsl_anat-399-fi
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-404-# output: ${T1}
fsl-5.0.8/src/misc_scripts/fsl_anat:405:minval=`$FSLDIR/bin/fslstats ${T1} -p 0`;
fsl-5.0.8/src/misc_scripts/fsl_anat:406:maxval=`$FSLDIR/bin/fslstats ${T1} -p 100`;
fsl-5.0.8/src/misc_scripts/fsl_anat:407:if [ X`echo "if ( $minval < 0 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/misc_scripts/fsl_anat:408: if [ X`echo "if ( $maxval > 0 ) { 1 }" | bc -l` = X1 ] ; then
fsl-5.0.8/src/misc_scripts/fsl_anat-409- # if there are just some negative values among the positive ones then reset zero to the min value
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-487- # make sure the overall scaling doesn't change (equate medians)
fsl-5.0.8/src/misc_scripts/fsl_anat:488: med0=`$FSLDIR/bin/fslstats ${T1} -k ${T1}_hpf_brain_mask -P 50`;
fsl-5.0.8/src/misc_scripts/fsl_anat:489: med1=`$FSLDIR/bin/fslstats ${T1}_hpf2_brain -k ${T1}_hpf_brain_mask -P 50`;
fsl-5.0.8/src/misc_scripts/fsl_anat-490- run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -div $med1 -mul $med0 ${T1}_hpf2_brain
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-601- fi
fsl-5.0.8/src/misc_scripts/fsl_anat:602: vscale=`${FSLDIR}/bin/avscale ${T1}2std_skullcon.mat | grep Determinant | awk '{ print $3 }'`;
fsl-5.0.8/src/misc_scripts/fsl_anat:603: ugrey=`$FSLDIR/bin/fslstats ${T1}_fast_pve_1 -m -v | awk '{ print $1 * $3 }'`;
fsl-5.0.8/src/misc_scripts/fsl_anat:604: ngrey=`echo "$ugrey * $vscale" | bc -l`;
fsl-5.0.8/src/misc_scripts/fsl_anat:605: uwhite=`$FSLDIR/bin/fslstats ${T1}_fast_pve_2 -m -v | awk '{ print $1 * $3 }'`;
fsl-5.0.8/src/misc_scripts/fsl_anat:606: nwhite=`echo "$uwhite * $vscale" | bc -l`;
fsl-5.0.8/src/misc_scripts/fsl_anat:607: ubrain=`echo "$ugrey + $uwhite" | bc -l`;
fsl-5.0.8/src/misc_scripts/fsl_anat:608: nbrain=`echo "$ngrey + $nwhite" | bc -l`;
fsl-5.0.8/src/misc_scripts/fsl_anat-609- echo "Scaling factor from ${T1} to MNI (using skull-constrained linear registration) = $vscale" > ${T1}_vols.txt
##############################################
fsl-5.0.8/src/misc_scripts/fsl_anat-626- # rather complicated way of making a link to a non-existent file or files (as FIRST may run on the cluster) - the alernative would be fsl_sub and job holds...
fsl-5.0.8/src/misc_scripts/fsl_anat:627: names=`$FSLDIR/bin/imglob -extensions ${T1}`;
fsl-5.0.8/src/misc_scripts/fsl_anat:628: for fn in $names ; do ext=`echo $fn | sed "s/${T1}.//"`;
fsl-5.0.8/src/misc_scripts/fsl_anat-629- run cp -r first_results/${T1}_first_all_fast_firstseg.${ext} ${T1}_subcort_seg.${ext}
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-270- #strip off extension from input file
fsl-5.0.8/src/oxford_asl/asl_calib:271: infile=`imglob $infile`
fsl-5.0.8/src/oxford_asl/asl_calib-272-
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-284-# make a temporary directory to work in - delete at end
fsl-5.0.8/src/oxford_asl/asl_calib:285:tmpbase=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/oxford_asl/asl_calib-286-temp_calib=${tmpbase}_asl_calib
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-471-# sort out the roi
fsl-5.0.8/src/oxford_asl/asl_calib:472:# xsize=`fslinfo $struc | grep "^dim1" | sed 's:dim1[ ]*::'`
fsl-5.0.8/src/oxford_asl/asl_calib:473:# ysize=`fslinfo $struc | grep "^dim2" | sed 's:dim2[ ]*::'`
fsl-5.0.8/src/oxford_asl/asl_calib:474:# zsize=`fslinfo $struc | grep "^dim3" | sed 's:dim3[ ]*::'`
fsl-5.0.8/src/oxford_asl/asl_calib-475-# roisize="0.3";
fsl-5.0.8/src/oxford_asl/asl_calib-476-#echo "$xsize $ysize $zsize $roisize"
fsl-5.0.8/src/oxford_asl/asl_calib:477:# delx=`echo "v = $roisize * $xsize; v /= 1; v" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib:478:# xmin=`echo "v = 0.5 * $xsize - $delx / 2; v /= 1; v" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib:479:# dely=`echo "v = $roisize * $ysize; v /= 1; v" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib:480:# ymin=`echo "v = 0.5 * $ysize - $dely / 2; v /= 1; v" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib:481:# delz=`echo "v = $roisize * $zsize; v /= 1; v" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib:482:# zmin=`echo "v = 0.5 * $zsize - $delz / 2 + 0.1; v /= 1; v" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib-483-# echo "$xmin $delx $ymin $dely $zmin $delz" >> $log
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-559-# cluster -i $temp_calib/refmask -t 0.9 -o $temp_calib/refmask_cluster --no_table
fsl-5.0.8/src/oxford_asl/asl_calib:560:# clusthr=`fslstats $temp_calib/refmask_cluster.nii.gz -R | awk '// {print $2}'`
fsl-5.0.8/src/oxford_asl/asl_calib:561:# clusthr=`echo "$clusthr - 1" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib-562-# echo "Clustering threshold: $clusthr" >> $log
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-571-#check there are some non-zero voxels
fsl-5.0.8/src/oxford_asl/asl_calib:572:nzvox=`fslstats $temp_calib/refmask -V | awk '{print \$1}'`
fsl-5.0.8/src/oxford_asl/asl_calib-573-echo "Number of voxels in tissue reference mask: $nzvox" >> $log
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-601- #cut - throw away first volume
fsl-5.0.8/src/oxford_asl/asl_calib:602: #tsize=`fslinfo $calib | grep "^dim4" | sed 's:dim4[ ]*::'`
fsl-5.0.8/src/oxford_asl/asl_calib-603- #fslroi $calib $temp_calib/calib 1 $tsize
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-616- # calculate M0_ref value
fsl-5.0.8/src/oxford_asl/asl_calib:617: Moval=`fslstats $temp_calib/calib -M` # this is Mz of CSF
fsl-5.0.8/src/oxford_asl/asl_calib:618: Moval=`echo "$Moval / (1 - e(- ( $tr - $taq ) / $T1r) )" | bc -l` #this is now M0 of the reference
fsl-5.0.8/src/oxford_asl/asl_calib-619- echo "Mz of reference tissue: $Moval" >> $log
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-634- tislist=""
fsl-5.0.8/src/oxford_asl/asl_calib:635: thetis=`echo $tis | sed 's:,: :g'`
fsl-5.0.8/src/oxford_asl/asl_calib-636- for ti in $thetis; do
fsl-5.0.8/src/oxford_asl/asl_calib:637: count=`expr ${count} + 1`
fsl-5.0.8/src/oxford_asl/asl_calib:638: tislist=`echo $tislist --ti${count}=$ti`
fsl-5.0.8/src/oxford_asl/asl_calib-639- done
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-664- # calculate M0 value
fsl-5.0.8/src/oxford_asl/asl_calib:665: Moval=`fslstats $temp_calib/satrecov/mean_M0t -M` # this is M0 of CSF at the TE of the sequence
fsl-5.0.8/src/oxford_asl/asl_calib-666- echo "M0 of reference tissue: $Moval" >> $log
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-693-#echo "$Moval $te $T2r $cgain $T2bl"
fsl-5.0.8/src/oxford_asl/asl_calib:694:Moval=`echo "$Moval / e(- $te / $T2r )" | bc -l` # T2 correction for M0 reference
fsl-5.0.8/src/oxford_asl/asl_calib-695-#echo $Moval
fsl-5.0.8/src/oxford_asl/asl_calib:696:Moval=`echo "scale=2;$Moval*$cgain / $pc" | bc` # this is M0 blood (at TE=0)
fsl-5.0.8/src/oxford_asl/asl_calib-697-#echo $Moval
fsl-5.0.8/src/oxford_asl/asl_calib:698:Moval=`echo "$Moval * e(- $te / $T2b )" | bc -l` # get M0 blood at TE used
fsl-5.0.8/src/oxford_asl/asl_calib-699-echo "M0:$Moval"
##############################################
fsl-5.0.8/src/oxford_asl/asl_calib-738-#save the calibration factor to the filename $outfact
fsl-5.0.8/src/oxford_asl/asl_calib:739: factor=`echo "scale=2; 6000 / $Moval" | bc`
fsl-5.0.8/src/oxford_asl/asl_calib-740- echo $factor > $outfact
##############################################
fsl-5.0.8/src/oxford_asl/asl_reg-144-# make a temporary directory to work in - delete at end
fsl-5.0.8/src/oxford_asl/asl_reg:145:tmpbase=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/oxford_asl/asl_reg-146-if [ -z $debug ]; then
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-252- if [ ! -z $pvexist ]; then #NB e we only do this is the PVE are available (and thus the reqd masks will exist)
fsl-5.0.8/src/oxford_asl/oxford_asl:253: repval=`${FSLDIR}/bin/fslstats $outdir/$subdir/native_space/$parname -k $tempdir/${masktype}mask_pure -m`
fsl-5.0.8/src/oxford_asl/oxford_asl-254- echo $repval > $outdir/$subdir/${parname}_${masktype}_mean.txt
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-268- # get normalization from reported value in the output directory
fsl-5.0.8/src/oxford_asl/oxford_asl:269: normval=`cat $outdir/$subdir/${parname}_${masktype}_mean.txt`
fsl-5.0.8/src/oxford_asl/oxford_asl-270-
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-291- # get normalization from reported value in the output directory
fsl-5.0.8/src/oxford_asl/oxford_asl:292: normval=`cat $outdir/$subdir/${parname}_${masktype}_mean.txt`
fsl-5.0.8/src/oxford_asl/oxford_asl-293- #need to square the value as we are outputting a variance
fsl-5.0.8/src/oxford_asl/oxford_asl:294: normval=`echo "$normval * $normval" | bc`
fsl-5.0.8/src/oxford_asl/oxford_asl-295-
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-434-# work out which is the final step from BASIL
fsl-5.0.8/src/oxford_asl/oxford_asl:435:finalstep=`ls -d $2/basil/step? | sed -n '$ p'`
fsl-5.0.8/src/oxford_asl/oxford_asl-436-echo "Using BASIL step $finalstep" >> $log
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-554- if [ $cmethod = 'single' ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl:555: malpha=`echo "$Mo * $alpha" | bc` #include the inversion efficiency when we do the final calibration
fsl-5.0.8/src/oxford_asl/oxford_asl-556- elif [ $cmethod = 'voxel' ]; then
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-574- if [ $cmethod = 'single' ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl:575: Mosq=`echo "$Mo * $Mo * $alpha * $alpha" | bc` #include the inversion efficiency when we do the final calibration
fsl-5.0.8/src/oxford_asl/oxford_asl-576- elif [ $cmethod = 'voxel' ]; then
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-625-# look at this option and determine if has an argument specified by an =
fsl-5.0.8/src/oxford_asl/oxford_asl:626:option=`echo $1 | sed s/=.*//`
fsl-5.0.8/src/oxford_asl/oxford_asl-627-arg="" #specifies if an argument is to be read from next item on command line (=1 is is when = is used)
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-633- arg=1
fsl-5.0.8/src/oxford_asl/oxford_asl:634: argument=`echo $1 | sed s/.*=//`
fsl-5.0.8/src/oxford_asl/oxford_asl-635-fi
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-774-# deal with the temporary directory
fsl-5.0.8/src/oxford_asl/oxford_asl:775:tmpbase=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/oxford_asl/oxford_asl-776-tempdir=${tmpbase}_ox_asl
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-822-else
fsl-5.0.8/src/oxford_asl/oxford_asl:823: if [ `${FSLDIR}/bin/imtest $infile` -eq 0 ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl-824- echo "ERROR: $infile is not an image/has not been found"
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-831- if [ ! -z $struc ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl:832: if [ `${FSLDIR}/bin/imtest $struc` -eq 0 ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl-833- echo "ERROR: $struc is not an image/has not been found"
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-848-if [ ! -z $lowstruc ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl:849: if [ `${FSLDIR}/bin/imtest $lowstruc` -eq 0 ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl-850- echo "ERROR: $lowstruc is not an image/has not been found"
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-900-if [ ! -z $calib ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl:901: tsize=`fslinfo $calib | grep "^dim4" | sed 's:dim4[ ]*::'`
fsl-5.0.8/src/oxford_asl/oxford_asl-902- if [ $tsize -gt 1 ]; then
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-904- Log "Removing first volume of calibration time series - to ensure data is in steady state"
fsl-5.0.8/src/oxford_asl/oxford_asl:905: tsize=`expr $tsize - 1`
fsl-5.0.8/src/oxford_asl/oxford_asl-906- fslroi $calib $tempdir/calib 1 $tsize
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1042-if [ ! -z $pvcorr ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl:1043: if [ `$FSLDIR/bin/imtest $tempdir/pvgm_inasl` -eq 0 ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl-1044- echo "ERROR: PV correction cannot be performed without either a structural image or supplied PVE"
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1096- Calibration
fsl-5.0.8/src/oxford_asl/oxford_asl:1097: Mo=`cat $outdir/calib/M0.txt`
fsl-5.0.8/src/oxford_asl/oxford_asl-1098- elif [ $cmethod = 'voxel' ]; then
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1103- Mo=$outdir/calib/M0
fsl-5.0.8/src/oxford_asl/oxford_asl:1104: if [ 1 -eq `echo "$tr < 5" | bc` ]; then
fsl-5.0.8/src/oxford_asl/oxford_asl-1105- # correct the M0 image for short TR using the equation from the white paper
fsl-5.0.8/src/oxford_asl/oxford_asl-1106- echo "Correcting the calibration (M0) image for short TR"
fsl-5.0.8/src/oxford_asl/oxford_asl:1107: ccorr=`echo "1 / (1 - e(- $tr / $t1set) )" | bc -l`
fsl-5.0.8/src/oxford_asl/oxford_asl-1108- ${FSLDIR}/bin/fslmaths $Mo -mul $ccorr $Mo
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1122-tislist=""
fsl-5.0.8/src/oxford_asl/oxford_asl:1123:thetis=`echo $tis | sed 's:,: :g'`
fsl-5.0.8/src/oxford_asl/oxford_asl-1124-#echo $thetis
fsl-5.0.8/src/oxford_asl/oxford_asl-1125-for ti in $thetis; do
fsl-5.0.8/src/oxford_asl/oxford_asl:1126: count=`expr ${count} + 1`
fsl-5.0.8/src/oxford_asl/oxford_asl:1127: tislist=`echo $tislist --ti${count}=$ti`
fsl-5.0.8/src/oxford_asl/oxford_asl:1128: alltis[`expr ${count} - 1`]=$ti
fsl-5.0.8/src/oxford_asl/oxford_asl-1129-done
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1132-#deal with repeats
fsl-5.0.8/src/oxford_asl/oxford_asl:1133:tpoints=`fslinfo $infile | grep "^dim4" | sed 's:dim4[ ]*::'`
fsl-5.0.8/src/oxford_asl/oxford_asl:1134:repeats=`expr $tpoints / $count`
fsl-5.0.8/src/oxford_asl/oxford_asl-1135-
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1143- for ((i=0; i<$count; i++)); do
fsl-5.0.8/src/oxford_asl/oxford_asl:1144: idx=`expr $r \* $count + $i`
fsl-5.0.8/src/oxford_asl/oxford_asl-1145- alltis[$idx]=${alltis[$i]}
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1191- asl_file --data=$infile --ntis=$count --ibf=rpt --iaf=diff --epoch=$tempdir/epoch --elen=$elen --eol=$eol --eunit=tis
fsl-5.0.8/src/oxford_asl/oxford_asl:1192: eadv=`expr $elen - $eol`
fsl-5.0.8/src/oxford_asl/oxford_asl-1193-fi
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1273- ${FSLDIR}/bin/fslmaths $datafile -Tmax $tempdir/datamax
fsl-5.0.8/src/oxford_asl/oxford_asl:1274: brain_mag=`${FSLDIR}/bin/fslstats $tempdir/datamax -k $tempdir/mask -M`
fsl-5.0.8/src/oxford_asl/oxford_asl-1275- # this will correspond to whole brain CBF (roughly) - about 0.5 of GM
fsl-5.0.8/src/oxford_asl/oxford_asl:1276: noisesd=`echo "scale=2;sqrt( $brain_mag * 2 / $snr )" | bc`
fsl-5.0.8/src/oxford_asl/oxford_asl-1277- fi
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1302-Log "----"
fsl-5.0.8/src/oxford_asl/oxford_asl:1303:Log "`cat $tempdir/basil_options.txt`"
fsl-5.0.8/src/oxford_asl/oxford_asl-1304-Log "----"
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1333- for ((ei=0; ei<$elen; ei++)); do
fsl-5.0.8/src/oxford_asl/oxford_asl:1334: ethis=`expr $ecount \* $eadv + $ei`
fsl-5.0.8/src/oxford_asl/oxford_asl-1335- #echo $ethis
fsl-5.0.8/src/oxford_asl/oxford_asl:1336: eidx=`expr $ei + 1`
fsl-5.0.8/src/oxford_asl/oxford_asl-1337- #echo $ei
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1350-
fsl-5.0.8/src/oxford_asl/oxford_asl:1351: ecount=`expr $ecount + 1`
fsl-5.0.8/src/oxford_asl/oxford_asl-1352- done
##############################################
fsl-5.0.8/src/oxford_asl/oxford_asl-1354-# produce an ftiss image to use for registration - mean of all the ftiss images over the epochs
fsl-5.0.8/src/oxford_asl/oxford_asl:1355:#fslmerge -t $tempdir/ftiss `ls $tempdir/epoch*/ftiss.nii.gz`
fsl-5.0.8/src/oxford_asl/oxford_asl-1356-fi
##############################################
fsl-5.0.8/src/oxford_asl/quasil-167- outdir=$outdir"+"
fsl-5.0.8/src/oxford_asl/quasil:168: count=`expr $count + 1`
fsl-5.0.8/src/oxford_asl/quasil-169-
##############################################
fsl-5.0.8/src/oxford_asl/quasil-181-# make a temp directory to work in
fsl-5.0.8/src/oxford_asl/quasil:182:tmpbase=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/src/oxford_asl/quasil-183-tempdir=${tmpbase}_quasil
##############################################
fsl-5.0.8/src/oxford_asl/quasil-193-tislist=""
fsl-5.0.8/src/oxford_asl/quasil:194:thetis=`echo $tis | sed 's:,: :g'`
fsl-5.0.8/src/oxford_asl/quasil-195-for ti in $thetis; do
fsl-5.0.8/src/oxford_asl/quasil:196: count=`expr ${count} + 1`
fsl-5.0.8/src/oxford_asl/quasil:197: tislist=`echo $tislist --ti${count}=$ti`
fsl-5.0.8/src/oxford_asl/quasil-198-done
##############################################
fsl-5.0.8/src/oxford_asl/quasil-250- mkdir ti$i
fsl-5.0.8/src/oxford_asl/quasil:251: tifile=`ls ti$i.nii.gz ti0$i.nii.gz ti00$i.nii.gz 2>/dev/null`
fsl-5.0.8/src/oxford_asl/quasil-252- echo $tifile
##############################################
fsl-5.0.8/src/oxford_asl/quasil-282-# we do not (currently) use this for the main analysis
fsl-5.0.8/src/oxford_asl/quasil:283:nkeep=`expr $ntis \* 6`
fsl-5.0.8/src/oxford_asl/quasil-284-fslroi asldata asldata 0 $nkeep
##############################################
fsl-5.0.8/src/oxford_asl/quasil-334- #fslmaths instruction for calibration (for execution whilst back in starting dir)
fsl-5.0.8/src/oxford_asl/quasil:335: cinstr=" -div `cat $tempdir/calib/M0a.txt` "
fsl-5.0.8/src/oxford_asl/quasil-336-
##############################################
fsl-5.0.8/src/fslio/immv-79-if [ $# -eq 2 -a ! -d $2 ] ; then
fsl-5.0.8/src/fslio/immv:80: f1=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/fslio/immv:81: f2=`${FSLDIR}/bin/remove_ext $2`;
fsl-5.0.8/src/fslio/immv-82- # do the moves
##############################################
fsl-5.0.8/src/fslio/immv-103- for fn in $flist ; do
fsl-5.0.8/src/fslio/immv:104: f1=`${FSLDIR}/bin/remove_ext $fn`;
fsl-5.0.8/src/fslio/immv-105- # do the copies
##############################################
fsl-5.0.8/src/fslio/imrm-78-for f in $@ ; do
fsl-5.0.8/src/fslio/imrm:79: fn=`${FSLDIR}/bin/remove_ext $f`;
fsl-5.0.8/src/fslio/imrm-80- # do the rm silently
##############################################
fsl-5.0.8/src/fslio/imln-78-
fsl-5.0.8/src/fslio/imln:79:f1=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/fslio/imln:80:f2=`${FSLDIR}/bin/remove_ext $2`;
fsl-5.0.8/src/fslio/imln-81-
##############################################
fsl-5.0.8/src/fslio/remove_ext-79- # for the ones at the end of the line
fsl-5.0.8/src/fslio/remove_ext:80: f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
fsl-5.0.8/src/fslio/remove_ext-81- # for the ones in the middle of the line
fsl-5.0.8/src/fslio/remove_ext:82: f=`echo "$f" | sed 's/\.hdr\.gz[ ]/ /g' | sed 's/\.img\.gz[ ]/ /g' | sed 's/\.hdr[ ]/ /g' | sed 's/\.img[ ]/ /g' | sed 's/\.nii\.gz[ ]/ /g' | sed 's/\.nii[ ]/ /g' | sed 's/\.mnc\.gz[ ]/ /g' | sed 's/\.mnc[ ]/ /g' |sed 's/\.[ ]/ /g'`;
fsl-5.0.8/src/fslio/remove_ext-83- lst="$lst $f";
##############################################
fsl-5.0.8/src/fslio/imtest-85-if [ -h $inputfile ] ; then
fsl-5.0.8/src/fslio/imtest:86:inputfile=`readlink $inputfile`;
fsl-5.0.8/src/fslio/imtest-87-fi
##############################################
fsl-5.0.8/src/fslio/imtest-89-
fsl-5.0.8/src/fslio/imtest:90:filename=`${FSLDIR}/bin/remove_ext $inputfile`;
fsl-5.0.8/src/fslio/imtest-91-
##############################################
fsl-5.0.8/src/fslio/imcp-80-if [ $# -eq 2 -a ! -d $2 ] ; then
fsl-5.0.8/src/fslio/imcp:81: f1=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/fslio/imcp:82: f2=`${FSLDIR}/bin/remove_ext $2`;
fsl-5.0.8/src/fslio/imcp-83- # do the copies
##############################################
fsl-5.0.8/src/fslio/imcp-104- for fn in $flist ; do
fsl-5.0.8/src/fslio/imcp:105: f1=`${FSLDIR}/bin/remove_ext $fn`;
fsl-5.0.8/src/fslio/imcp-106- # do the copies
##############################################
fsl-5.0.8/src/qboot/qboot_preproc.sh-71-
fsl-5.0.8/src/qboot/qboot_preproc.sh:72:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
fsl-5.0.8/src/qboot/qboot_preproc.sh-73- ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.qboot/nodif_brain
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-106-
fsl-5.0.8/src/qboot/qboot_parallel:107:subjdir=`make_absolute $1`
fsl-5.0.8/src/qboot/qboot_parallel:108:subjdir=`echo $subjdir | sed 's/\/$/$/g'`
fsl-5.0.8/src/qboot/qboot_parallel-109-
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-131-
fsl-5.0.8/src/qboot/qboot_parallel:132:if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
fsl-5.0.8/src/qboot/qboot_parallel-133- echo "${subjdir}/data not found"
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-137-
fsl-5.0.8/src/qboot/qboot_parallel:138:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
fsl-5.0.8/src/qboot/qboot_parallel-139- echo "${subjdir}/nodif_brain_mask not found"
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-151-echo Queuing preprocessing stages
fsl-5.0.8/src/qboot/qboot_parallel:152:preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -N qboot_preproc -l ${subjdir}.qboot/logs ${FSLDIR}/bin/qboot_preproc.sh ${subjdir}`
fsl-5.0.8/src/qboot/qboot_parallel-153-
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-155-echo Queuing parallel processing stage
fsl-5.0.8/src/qboot/qboot_parallel:156:nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
fsl-5.0.8/src/qboot/qboot_parallel-157-[ -f ${subjdir}.qboot/commands.txt ] && rm ${subjdir}.qboot/commands.txt
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-161- do
fsl-5.0.8/src/qboot/qboot_parallel:162: slicezp=`$FSLDIR/bin/zeropad $slice 4`
fsl-5.0.8/src/qboot/qboot_parallel:163: if [ `$FSLDIR/bin/imtest ${subjdir}.qboot/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_parallel-164- echo "slice $slice has already been processed"
##############################################
fsl-5.0.8/src/qboot/qboot_parallel-170-
fsl-5.0.8/src/qboot/qboot_parallel:171: qbootid=`${FSLDIR}/bin/fsl_sub -q long.q -j $preprocid -l ${subjdir}.qboot/logs -N qboot -t ${subjdir}.qboot/commands.txt`
fsl-5.0.8/src/qboot/qboot_parallel-172-
fsl-5.0.8/src/qboot/qboot_parallel-173- echo Queuing post processing stage
fsl-5.0.8/src/qboot/qboot_parallel:174: mergeid=`${FSLDIR}/bin/fsl_sub -j $qbootid -T 60 -N qboot_postproc -l ${subjdir}.qboot/logs ${FSLDIR}/bin/qboot_postproc.sh $subjdir`
##############################################
fsl-5.0.8/src/qboot/qboot_postproc.sh-67-
fsl-5.0.8/src/qboot/qboot_postproc.sh:68:numfib=`${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_0000/merged_f*samples* | wc -w | awk '{print $1}'`
fsl-5.0.8/src/qboot/qboot_postproc.sh-69-
##############################################
fsl-5.0.8/src/qboot/qboot_postproc.sh-72-do
fsl-5.0.8/src/qboot/qboot_postproc.sh:73: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/merged_th${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/merged_th${fib}samples*`
fsl-5.0.8/src/qboot/qboot_postproc.sh:74: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/merged_ph${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/merged_ph${fib}samples*`
fsl-5.0.8/src/qboot/qboot_postproc.sh:75: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/merged_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/merged_f${fib}samples*`
fsl-5.0.8/src/qboot/qboot_postproc.sh:76: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/dyads${fib} `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/dyads${fib}*`
fsl-5.0.8/src/qboot/qboot_postproc.sh:77: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/mean_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/mean_f${fib}samples*`
fsl-5.0.8/src/qboot/qboot_postproc.sh-78- ${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.qboot/merged_th${fib}samples ${subjdir}.qboot/merged_ph${fib}samples ${subjdir}.qboot/nodif_brain_mask ${subjdir}.qboot/dyads${fib}
##############################################
fsl-5.0.8/src/qboot/qboot_postproc.sh-82-
fsl-5.0.8/src/qboot/qboot_postproc.sh:83:if [ `${FSLDIR}/bin/imtest ${subjdir}.qboot/diff_slices/data_slice_0000/meanSHcoeff` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_postproc.sh:84: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/mean_SHcoeff `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/meanSHcoeff*`
fsl-5.0.8/src/qboot/qboot_postproc.sh-85-fi
fsl-5.0.8/src/qboot/qboot_postproc.sh-86-
fsl-5.0.8/src/qboot/qboot_postproc.sh:87:if [ `${FSLDIR}/bin/imtest ${subjdir}.qboot/diff_slices/data_slice_0000/GFA` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_postproc.sh:88: ${FSLDIR}/bin/fslmerge -z ${subjdir}.qboot/GFA `${FSLDIR}/bin/imglob ${subjdir}.qboot/diff_slices/data_slice_*/GFA*`
fsl-5.0.8/src/qboot/qboot_postproc.sh-89-fi
##############################################
fsl-5.0.8/src/qboot/qboot_postproc.sh-93-
fsl-5.0.8/src/qboot/qboot_postproc.sh:94:if [ `${FSLDIR}/bin/imtest ${subjdir}.qboot/merged_th1samples` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_postproc.sh:95: if [ `imtest ${subjdir}.qboot/merged_ph1samples` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_postproc.sh:96: if [ `imtest ${subjdir}.qboot/merged_f1samples` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_postproc.sh-97- rm -rf ${subjdir}.qboot/diff_slices
##############################################
fsl-5.0.8/src/qboot/qboot_postproc.sh-103-
fsl-5.0.8/src/qboot/qboot_postproc.sh:104:if [ `${FSLDIR}/bin/imtest ${subjdir}.qboot/mean_SHcoeff` -eq 1 ];then
fsl-5.0.8/src/qboot/qboot_postproc.sh-105- rm -rf ${subjdir}.qboot/diff_slices
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-170-export POSIXLY_CORRECT
fsl-5.0.8/src/sgeutils/fsl_sub:171:command=`basename $0`
fsl-5.0.8/src/sgeutils/fsl_sub-172-
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-229-
fsl-5.0.8/src/sgeutils/fsl_sub:230:set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`
fsl-5.0.8/src/sgeutils/fsl_sub-231-result=$?
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-303- -z)
fsl-5.0.8/src/sgeutils/fsl_sub:304: if [ -e $2 -o `${FSLDIR}/bin/imtest $2` = 1 ] ; then
fsl-5.0.8/src/sgeutils/fsl_sub-305- exit 0
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-321- acceptable_arch=no
fsl-5.0.8/src/sgeutils/fsl_sub:322: available_archs=`qhost | tail -n +4 | awk '{print $2}' | sort | uniq`
fsl-5.0.8/src/sgeutils/fsl_sub-323- for a in $available_archs; do
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-348- if [ -f "$taskfile" ] ; then
fsl-5.0.8/src/sgeutils/fsl_sub:349: tasks=`wc -l $taskfile | awk '{print $1}'`
fsl-5.0.8/src/sgeutils/fsl_sub-350- if [ $tasks -ne 0 ]; then
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-388- pe_string=$2;
fsl-5.0.8/src/sgeutils/fsl_sub:389: peName=`echo $pe_string | cut -d',' -f 1`
fsl-5.0.8/src/sgeutils/fsl_sub:390: peThreads=`echo $pe_string | cut -d',' -f 2`
fsl-5.0.8/src/sgeutils/fsl_sub-391- shift;;
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-415- if [ "x$taskfile" != x ] ; then
fsl-5.0.8/src/sgeutils/fsl_sub:416: JobName=`basename $taskfile`
fsl-5.0.8/src/sgeutils/fsl_sub-417- else
fsl-5.0.8/src/sgeutils/fsl_sub:418: JobName=`basename $1`
fsl-5.0.8/src/sgeutils/fsl_sub-419- fi
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-510-
fsl-5.0.8/src/sgeutils/fsl_sub:511:command=\`sed -n -e "\${SGE_TASK_ID}p" $taskfile\`
fsl-5.0.8/src/sgeutils/fsl_sub-512-
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-543- while [ $n -le $tasks ] ; do
fsl-5.0.8/src/sgeutils/fsl_sub:544: line=`sed -n -e ''${n}'p' $taskfile`
fsl-5.0.8/src/sgeutils/fsl_sub-545- if [ $verbose -eq 1 ] ; then
##############################################
fsl-5.0.8/src/sgeutils/fsl_sub-550-EOF2
fsl-5.0.8/src/sgeutils/fsl_sub:551: n=`expr $n + 1`
fsl-5.0.8/src/sgeutils/fsl_sub-552- done
##############################################
fsl-5.0.8/src/miscvis/slices-89-# if statement checks if -o option was given
fsl-5.0.8/src/miscvis/slices:90:if [ `echo "$@" | grep -- -o | wc -w` -gt 0 ] ; then
fsl-5.0.8/src/miscvis/slices-91- # extract the <output gif> name if the -o option is present
fsl-5.0.8/src/miscvis/slices:92: outputname=`echo "$@" | sed 's/.*-o *\([^ ]*\).*/\1/'`;
fsl-5.0.8/src/miscvis/slices-93-fi
fsl-5.0.8/src/miscvis/slices-94-
fsl-5.0.8/src/miscvis/slices:95:if [ `$FSLDIR/bin/imtest $1` -eq 0 ] ; then
fsl-5.0.8/src/miscvis/slices-96-echo "cannot read file $1"
##############################################
fsl-5.0.8/src/miscvis/slices-99-
fsl-5.0.8/src/miscvis/slices:100:f=`${FSLDIR}/bin/tmpnam /tmp/\`${FSLDIR}/bin/remove_ext $1 | sed "s/\//_/g"\``
fsl-5.0.8/src/miscvis/slices-101-
fsl-5.0.8/src/miscvis/slices-102-# deal with complex images separately
fsl-5.0.8/src/miscvis/slices:103:if [ X`${FSLDIR}/bin/fslval $1 datatype` = X32 ] ; then
fsl-5.0.8/src/miscvis/slices-104- nm1=${f}_abs
fsl-5.0.8/src/miscvis/slices-105- nm2=${f}_ph
fsl-5.0.8/src/miscvis/slices:106: nm0=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/miscvis/slices-107- if [ X$1 != X ] ; then
##############################################
fsl-5.0.8/src/miscvis/slices-118-
fsl-5.0.8/src/miscvis/slices:119:if [ X`${FSLDIR}/bin/fslval $1 dim3` = X1 ] ; then
fsl-5.0.8/src/miscvis/slices-120- # 2D case
fsl-5.0.8/src/miscvis/slices-121- slicenum=-0
fsl-5.0.8/src/miscvis/slices:122: im1=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/miscvis/slices-123- if [ X$2 != X ] ; then
fsl-5.0.8/src/miscvis/slices-124- shift ;
fsl-5.0.8/src/miscvis/slices:125: im2=`${FSLDIR}/bin/remove_ext $1`;
fsl-5.0.8/src/miscvis/slices-126- fi
##############################################
fsl-5.0.8/src/miscvis/slices-130- if [ X$im2 != X ] ; then
fsl-5.0.8/src/miscvis/slices:131: if [ `$FSLDIR/bin/imtest $im2` -eq 1 ] ; then
fsl-5.0.8/src/miscvis/slices-132- # make a stacked version for getting edges
##############################################
fsl-5.0.8/src/miscvis/slices-143- # remove the "-o <output gif>" from the command line list
fsl-5.0.8/src/miscvis/slices:144: opts=`echo $opts | sed 's/-o *[^ ]*//'`;
fsl-5.0.8/src/miscvis/slices-145- if ${FSLDIR}/bin/slicer $im1 $im2 $opts -z $slicenum ${f}a.png ; then
##############################################
fsl-5.0.8/src/miscvis/slices-157- # remove the "-o <output gif>" from the command line list
fsl-5.0.8/src/miscvis/slices:158: opts=`echo $opts | sed 's/-o *[^ ]*//'`;
fsl-5.0.8/src/miscvis/slices-159-
##############################################
fsl-5.0.8/src/miscvis/slices-176- elif [ X`uname | grep -i darwin`X != XX ] ; then
fsl-5.0.8/src/miscvis/slices:177: g=`${FSLDIR}/bin/tmpnam $f`.gif ;
fsl-5.0.8/src/miscvis/slices-178- cp $f $g ;
##############################################
fsl-5.0.8/src/miscvis/slicesdir-113-
fsl-5.0.8/src/miscvis/slicesdir:114:number=`echo $* | wc -w`
fsl-5.0.8/src/miscvis/slicesdir-115-
##############################################
fsl-5.0.8/src/miscvis/slicesdir-118-
fsl-5.0.8/src/miscvis/slicesdir:119: A=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/miscvis/slicesdir-120- echo $A
##############################################
fsl-5.0.8/src/miscvis/slicesdir-123- ${FSLDIR}/bin/slicer $A $pairimage -s 1 $sliceropts
fsl-5.0.8/src/miscvis/slicesdir:124: Q=`echo $A | sed "s/\//_/g"`
fsl-5.0.8/src/miscvis/slicesdir-125- else
fsl-5.0.8/src/miscvis/slicesdir:126: B=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/miscvis/slicesdir-127- ${FSLDIR}/bin/slicer $A $B -s 1 $sliceropts
fsl-5.0.8/src/miscvis/slicesdir:128: Q=`echo $A | sed "s/\//_/g"`_to_`echo $B | sed "s/\//_/g"`
fsl-5.0.8/src/miscvis/slicesdir-129- fi
##############################################
fsl-5.0.8/src/miscvis/slicesdir-135- shift
fsl-5.0.8/src/miscvis/slicesdir:136: i=`echo "$i 1 + p" | dc -`
fsl-5.0.8/src/miscvis/slicesdir-137- if [ $Compare = 1 ] ; then
fsl-5.0.8/src/miscvis/slicesdir-138- shift
fsl-5.0.8/src/miscvis/slicesdir:139: i=`echo "$i 1 + p" | dc -`
fsl-5.0.8/src/miscvis/slicesdir-140- fi
##############################################
fsl-5.0.8/src/miscvis/slicesmask-80-
fsl-5.0.8/src/miscvis/slicesmask:81:A=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/miscvis/slicesmask:82:B=`${FSLDIR}/bin/remove_ext $2`
fsl-5.0.8/src/miscvis/slicesmask:83:C=`${FSLDIR}/bin/remove_ext $3`
fsl-5.0.8/src/miscvis/slicesmask-84-
fsl-5.0.8/src/miscvis/slicesmask:85:${FSLDIR}/bin/fslmaths $B -thr `${FSLDIR}/bin/fslstats $B -P 10` -bin -mul -1 -add 1 $C
fsl-5.0.8/src/miscvis/slicesmask-86-${FSLDIR}/bin/distancemap -i $C -o $C
fsl-5.0.8/src/miscvis/slicesmask-87-
fsl-5.0.8/src/miscvis/slicesmask:88:coords=`${FSLDIR}/bin/fslstats $C -x`
fsl-5.0.8/src/miscvis/slicesmask-89-
fsl-5.0.8/src/miscvis/slicesmask:90:X=`echo $coords | awk '{print $1}'`
fsl-5.0.8/src/miscvis/slicesmask:91:Y=`echo $coords | awk '{print $2}'`
fsl-5.0.8/src/miscvis/slicesmask:92:Z=`echo $coords | awk '{print $3}'`
fsl-5.0.8/src/miscvis/slicesmask-93-#echo $X $Y $Z
fsl-5.0.8/src/miscvis/slicesmask-94-
fsl-5.0.8/src/miscvis/slicesmask:95:if [ `${FSLDIR}/bin/fslstats $C -V | awk '{print $1}'` -ge 30 ] ; then
fsl-5.0.8/src/miscvis/slicesmask-96- chequer="-c"
##############################################
fsl-5.0.8/src/miscvis/slices_summary-97-
fsl-5.0.8/src/miscvis/slices_summary:98:if [ `${FSLDIR}/bin/imtest $1` = 1 ] ; then
fsl-5.0.8/src/miscvis/slices_summary-99-
##############################################
fsl-5.0.8/src/miscvis/slices_summary-103-
fsl-5.0.8/src/miscvis/slices_summary:104: in=`${FSLDIR}/bin/remove_ext $1`
fsl-5.0.8/src/miscvis/slices_summary:105: if [ `${FSLDIR}/bin/imtest $in` = 0 ] ; then
fsl-5.0.8/src/miscvis/slices_summary-106- echo "Input image $in not found"
##############################################
fsl-5.0.8/src/miscvis/slices_summary-110- bg=$3
fsl-5.0.8/src/miscvis/slices_summary:111: if [ `${FSLDIR}/bin/imtest $bg` = 0 ] ; then
fsl-5.0.8/src/miscvis/slices_summary-112- echo "Background image $bg not found"
##############################################
fsl-5.0.8/src/miscvis/slices_summary-125-
fsl-5.0.8/src/miscvis/slices_summary:126: bgdimx=`${FSLDIR}/bin/fslval $bg dim1`
fsl-5.0.8/src/miscvis/slices_summary:127: bgdimy=`${FSLDIR}/bin/fslval $bg dim2`
fsl-5.0.8/src/miscvis/slices_summary:128: bgrange=`${FSLDIR}/bin/fslstats $bg -l 0.01 -r`
fsl-5.0.8/src/miscvis/slices_summary-129-
fsl-5.0.8/src/miscvis/slices_summary:130: uthresh=`${FSLDIR}/bin/fslstats $in -l 0.01 -P 50`
fsl-5.0.8/src/miscvis/slices_summary:131: uthresh=`${FSLDIR}/bin/fslstats $in -l $uthresh -P 99.9`
fsl-5.0.8/src/miscvis/slices_summary-132- echo "Upper threshold is $uthresh"
##############################################
fsl-5.0.8/src/miscvis/slices_summary-135- cd $out
fsl-5.0.8/src/miscvis/slices_summary:136: for grot in `${FSLDIR}/bin/imglob vol*` ; do
fsl-5.0.8/src/miscvis/slices_summary:137: DD=`echo $grot | awk -F vol '{print $2}'`
fsl-5.0.8/src/miscvis/slices_summary-138- fslecho "[$DD \c"
##############################################
fsl-5.0.8/src/miscvis/slices_summary-140- /bin/rm -f grot.txt
fsl-5.0.8/src/miscvis/slices_summary:141: for g in `${FSLDIR}/bin/imglob grot_*` ; do
fsl-5.0.8/src/miscvis/slices_summary-142- ${FSLDIR}/bin/cluster -i $g -t $lthresh --osize=grot --no_table
fsl-5.0.8/src/miscvis/slices_summary-143- ${FSLDIR}/bin/fslmaths grot -sqrt -recip -mul $g -Xmean -Ymean grot -odt float
fsl-5.0.8/src/miscvis/slices_summary:144: echo "$g `${FSLDIR}/bin/fslstats grot -m`" >> grot.txt
fsl-5.0.8/src/miscvis/slices_summary-145- done
fsl-5.0.8/src/miscvis/slices_summary-146-
fsl-5.0.8/src/miscvis/slices_summary:147: best=`cat grot.txt | sort -k 2 -n | tail -n 1 | awk '{print $1}'`
fsl-5.0.8/src/miscvis/slices_summary:148: nbest=`${FSLDIR}/bin/remove_ext $best | awk -F _ '{print $2}'`
fsl-5.0.8/src/miscvis/slices_summary-149- ${FSLDIR}/bin/fslroi BG grot 0 $bgdimx 0 $bgdimy $nbest 1
##############################################
fsl-5.0.8/src/miscvis/slices_summary-153- if [ $allthree = 1 ] ; then
fsl-5.0.8/src/miscvis/slices_summary:154: lbest=`echo "$nbest 4 - p" | dc -`
fsl-5.0.8/src/miscvis/slices_summary-155- if [ $lbest -lt 1 ] ; then lbest=1; fi;
fsl-5.0.8/src/miscvis/slices_summary:156: lbest=`cat grot.txt | head -n $lbest | sort -k 2 -n | tail -n 1 | awk '{print $1}'`
fsl-5.0.8/src/miscvis/slices_summary:157: nlbest=`${FSLDIR}/bin/remove_ext $lbest | awk -F _ '{print $2}'`
fsl-5.0.8/src/miscvis/slices_summary-158- ${FSLDIR}/bin/fslroi BG grot 0 $bgdimx 0 $bgdimy $nlbest 1
##############################################
fsl-5.0.8/src/miscvis/slices_summary-160-
fsl-5.0.8/src/miscvis/slices_summary:161: ubest=`echo "$nbest 6 + p" | dc -`
fsl-5.0.8/src/miscvis/slices_summary-162- if [ $ubest -gt `cat grot.txt | wc -l` ] ; then ubest=`cat grot.txt | wc -l`; fi;
fsl-5.0.8/src/miscvis/slices_summary:163: ubest=`cat grot.txt | tail -n +$ubest | sort -k 2 -n | tail -n 1 | awk '{print $1}'`
fsl-5.0.8/src/miscvis/slices_summary:164: nubest=`${FSLDIR}/bin/remove_ext $ubest | awk -F _ '{print $2}'`
fsl-5.0.8/src/miscvis/slices_summary-165- ${FSLDIR}/bin/fslroi BG grot 0 $bgdimx 0 $bgdimy $nubest 1
##############################################
fsl-5.0.8/src/miscvis/slices_summary-172-
fsl-5.0.8/src/miscvis/slices_summary:173: ${FSLDIR}/bin/slicer grotB -u -z 0 `zeropad $DD 4`.png
fsl-5.0.8/src/miscvis/slices_summary-174- done
##############################################
fsl-5.0.8/src/miscvis/slices_summary-192- shift
fsl-5.0.8/src/miscvis/slices_summary:193: thestring="$thestring ${in}/`${FSLDIR}/bin/zeropad $s 4`.png +"
fsl-5.0.8/src/miscvis/slices_summary-194- done
fsl-5.0.8/src/miscvis/slices_summary-195- s=$1
fsl-5.0.8/src/miscvis/slices_summary:196: thestring="$thestring ${in}/`${FSLDIR}/bin/zeropad $s 4`.png $out"
fsl-5.0.8/src/miscvis/slices_summary-197- $thestring
##############################################
fsl-5.0.8/src/filmbabe/filmbabescript-99-
fsl-5.0.8/src/filmbabe/filmbabescript:100:files=`$FSLDIR/bin/imglob zfstat*.*`
fsl-5.0.8/src/filmbabe/filmbabescript:101:files=`$FSLDIR/bin/remove_ext $files`
fsl-5.0.8/src/filmbabe/filmbabescript-102-
##############################################
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-67-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:68:numfib=`${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples* | wc -w | awk '{print $1}'`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-69-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:70:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/f0samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-71- numfib=$(($numfib - 1))
##############################################
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-76-do
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:77: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:78: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:79: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-80- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
##############################################
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-92-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:93:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-94- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsumsamples
##############################################
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-103-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:104:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_dsamples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:105: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_dsamples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_dsamples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-106-fi
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-107-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:108:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_d_stdsamples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:109: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_d_stdsamples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_d_stdsamples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-110-fi
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-111-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:112:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_f0samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:113: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_f0samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_f0samples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-114-fi
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-115-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:116:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_S0samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:117: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_S0samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_S0samples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-118-fi
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-119-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:120:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_tausamples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:121: ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_tausamples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_tausamples*`
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-122-fi
##############################################
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-126-
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:127:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:128: if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:129: if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-130- rm -rf ${subjdir}.bedpostX/diff_slices
##############################################
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-132- rm -f ${subjdir}/nodif_brain_mask_slice_*
fsl-5.0.8/src/fdt/bedpostx_postproc.sh:133: if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev_slice_0000` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_postproc.sh-134- rm -f ${subjdir}/grad_dev_slice_*
##############################################
fsl-5.0.8/src/fdt/eddy_correct-82-
fsl-5.0.8/src/fdt/eddy_correct:83:input=`${FSLDIR}/bin/remove_ext ${1}`
fsl-5.0.8/src/fdt/eddy_correct:84:output=`${FSLDIR}/bin/remove_ext ${2}`
fsl-5.0.8/src/fdt/eddy_correct-85-ref=${3}
fsl-5.0.8/src/fdt/eddy_correct-86-
fsl-5.0.8/src/fdt/eddy_correct:87:if [ `${FSLDIR}/bin/imtest $input` -eq 0 ];then
fsl-5.0.8/src/fdt/eddy_correct-88- echo "Input does not exist or is not in a supported format"
##############################################
fsl-5.0.8/src/fdt/eddy_correct-94-fslsplit $input ${output}_tmp
fsl-5.0.8/src/fdt/eddy_correct:95:full_list=`${FSLDIR}/bin/imglob ${output}_tmp????.*`
fsl-5.0.8/src/fdt/eddy_correct-96-
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-125- part=0
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:126: errorFiles=\`ls ${subjdir}.bedpostX/logs/*.e* 2> /dev/null \`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-127- for errorFile in \$errorFiles
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-155- if [ "x$SGE_ROOT" == "x" ]; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:156: havedad=\`ps -e -o pid | grep "$$\\b" | wc -l\`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-157- fi
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-178-
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:179:subjdir=`make_absolute $1`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:180:subjdir=`echo $subjdir | sed 's/\/$/$/g'`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-181-
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-239-
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:240:if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-241- echo "${subjdir}/data not found"
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-245-if [ ${gflag} -eq 1 ]; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:246: if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev` -eq 0 ]; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-247- echo "${subjdir}/grad_dev not found"
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-251-
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:252:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-253- echo "${subjdir}/nodif_brain_mask not found"
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-277-${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:278:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-279- ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-281-
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:282:nvox=`${FSLDIR}/bin/fslstats $subjdir.bedpostX/nodif_brain_mask -V | cut -d ' ' -f1 `
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-283-
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-294-do
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:295: partzp=`$FSLDIR/bin/zeropad $part 4`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-296-
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-306-
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:307:bedpostid=`${FSLDIR}/bin/fsl_sub $queue -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx_gpu -t ${subjdir}.bedpostX/commands.txt`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-308-
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-309-echo Queuing post processing stage
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu:310:mergeid=`${FSLDIR}/bin/fsl_sub $queue -j $bedpostid -m ase -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc_gpu.sh --data=${subjdir}/data --mask=$subjdir.bedpostX/nodif_brain_mask -b ${subjdir}.bedpostX/bvals -r ${subjdir}.bedpostX/bvecs --forcedir --logdir=$subjdir.bedpostX/diff_parts $gopts $nvox $njobs ${subjdir}`
fsl-5.0.8/src/fdt/CUDA/bedpostx_gpu-311-
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-72- if [[ $arg =~ "--nf=" ]]; then
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh:73: numfib=`echo $arg | cut -d '=' -f2`
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-74- fi
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-94-
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh:95:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-96- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsumsamples
##############################################
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-108-
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh:109:if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh:110: if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh:111: if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-112- rm -rf ${subjdir}.bedpostX/diff_parts
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh:113: if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/grad_dev_slice_0000` -eq 1 ];then
fsl-5.0.8/src/fdt/CUDA/bedpostx_postproc_gpu.sh-114- rm -f ${subjdir}.bedpostX/grad_dev_slice_*
##############################################
fsl-5.0.8/src/fdt/post_xfibres-82-cd $dirname
fsl-5.0.8/src/fdt/post_xfibres:83:numfib=`${FSLDIR}/bin/imglob *f*samples* |wc -w`
fsl-5.0.8/src/fdt/post_xfibres-84-
##############################################
fsl-5.0.8/src/fdt/post_xfibres-86-fib=1;
fsl-5.0.8/src/fdt/post_xfibres:87:${FSLDIR}/bin/fslroi `${FSLDIR}/bin/imglob *f1samples*` numfibs 0 1
fsl-5.0.8/src/fdt/post_xfibres-88-${FSLDIR}/bin/fslmaths numfibs -mul 0 numfibs
##############################################
fsl-5.0.8/src/fdt/post_xfibres-90- echo $fib
fsl-5.0.8/src/fdt/post_xfibres:91: ${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/imglob *f${fib}samples*` -Tmean mean_f${fib}samples
fsl-5.0.8/src/fdt/post_xfibres-92- ${FSLDIR}/bin/fslmaths mean_f${fib}samples -thr $thresh -bin ${$}bin${fib}
fsl-5.0.8/src/fdt/post_xfibres-93- ${FSLDIR}/bin/fslmaths numfibs -add ${$}bin${fib} numfibs
fsl-5.0.8/src/fdt/post_xfibres:94: ${FSLDIR}/bin/make_dyadic_vectors `${FSLDIR}/bin/imglob *th${fib}samples*` `${FSLDIR}/bin/imglob *ph${fib}samples*` dyads${fib}
fsl-5.0.8/src/fdt/post_xfibres:95: fib=`echo "$fib +1"|bc`;
fsl-5.0.8/src/fdt/post_xfibres-96-done
##############################################
fsl-5.0.8/src/fdt/correct_and_average-79-[ $# -lt 2 ] && usage
fsl-5.0.8/src/fdt/correct_and_average:80:data=`remove_ext ${1}`;
fsl-5.0.8/src/fdt/correct_and_average-81-
fsl-5.0.8/src/fdt/correct_and_average-82-
fsl-5.0.8/src/fdt/correct_and_average:83:if [ `imtest $data` -eq 0 ];then
fsl-5.0.8/src/fdt/correct_and_average-84- echo "Cannot find image called $1";
##############################################
fsl-5.0.8/src/fdt/correct_and_average-92-
fsl-5.0.8/src/fdt/correct_and_average:93:numlines=`cat $avgfile |grep -v '^ *$'|wc -l`;
fsl-5.0.8/src/fdt/correct_and_average:94:numavgs=`expr $numlines - 1`;
fsl-5.0.8/src/fdt/correct_and_average:95:scans_per_avg=`cat $avgfile |sed 's/, *$/ /g'|sed 's/[^,]/ /g'|sed -n '1p'|wc -w`;
fsl-5.0.8/src/fdt/correct_and_average:96:scans_per_avg=`expr $scans_per_avg + 1`
fsl-5.0.8/src/fdt/correct_and_average:97:b0_numbers=`cat $avgfile |grep -v '^ *$' |sed -n "${numlines}p"`;
fsl-5.0.8/src/fdt/correct_and_average-98-
fsl-5.0.8/src/fdt/correct_and_average-99-
fsl-5.0.8/src/fdt/correct_and_average:100:ab0=`echo $b0_numbers |awk '{print \$1}'`
fsl-5.0.8/src/fdt/correct_and_average-101-eddy_correct ${1} ${$}${1}_b0_correct $ab0
fsl-5.0.8/src/fdt/correct_and_average:102:total_vols=`fslval $1 dim4`;
fsl-5.0.8/src/fdt/correct_and_average:103:vols_per_avg=`echo "10k $total_vols $numavgs / p"|dc -`;
fsl-5.0.8/src/fdt/correct_and_average-104-fslroi ${1} data 0 ${vols_per_avg};
##############################################
fsl-5.0.8/src/fdt/correct_and_average-113-
fsl-5.0.8/src/fdt/correct_and_average:114: tmp=`cat $avgfile |sed -n "${avg}p"|awk -F , "{ print \\$$scan }"`;
fsl-5.0.8/src/fdt/correct_and_average-115-
##############################################
fsl-5.0.8/src/fdt/correct_and_average-118- fslroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
fsl-5.0.8/src/fdt/correct_and_average:119: scan=`expr $scan + 1`;
fsl-5.0.8/src/fdt/correct_and_average-120- done
fsl-5.0.8/src/fdt/correct_and_average:121: fslmerge -t ${$}avg_${avg}_all `imglob ${$}avg_${avg}_scan_*`
fsl-5.0.8/src/fdt/correct_and_average-122- fslmaths data -add ${$}avg_${avg}_all data;
fsl-5.0.8/src/fdt/correct_and_average:123: avg=`expr $avg + 1`;
fsl-5.0.8/src/fdt/correct_and_average-124-
##############################################
fsl-5.0.8/src/fdt/ec_plot-3-if [ $# -lt 1 ] ; then
fsl-5.0.8/src/fdt/ec_plot:4: echo "Usage: `basename $0` <eddy current ecclog file>"
fsl-5.0.8/src/fdt/ec_plot-5- exit 0;
##############################################
fsl-5.0.8/src/fdt/ec_plot-8-logfile=$1;
fsl-5.0.8/src/fdt/ec_plot:9:basenm=`basename $logfile .ecclog`;
fsl-5.0.8/src/fdt/ec_plot-10-
fsl-5.0.8/src/fdt/ec_plot:11:nums=`grep -n 'Final' $logfile | sed 's/:.*//'`;
fsl-5.0.8/src/fdt/ec_plot-12-
##############################################
fsl-5.0.8/src/fdt/ec_plot-19- echo "Timepoint $m"
fsl-5.0.8/src/fdt/ec_plot:20: n1=`echo $n + 1 | bc` ;
fsl-5.0.8/src/fdt/ec_plot:21: n2=`echo $n + 5 | bc` ;
fsl-5.0.8/src/fdt/ec_plot-22- sed -n "$n1,${n2}p" $logfile > grot.mat ;
fsl-5.0.8/src/fdt/ec_plot-23- if [ $firsttime = yes ] ; then firsttime=no; cp grot.mat grot.refmat ; cp grot.mat grot.oldmat ; fi
fsl-5.0.8/src/fdt/ec_plot:24: absval=`$FSLDIR/bin/rmsdiff grot.mat grot.refmat $basenm`;
fsl-5.0.8/src/fdt/ec_plot:25: relval=`$FSLDIR/bin/rmsdiff grot.mat grot.oldmat $basenm`;
fsl-5.0.8/src/fdt/ec_plot-26- cp grot.mat grot.oldmat
##############################################
fsl-5.0.8/src/fdt/ec_plot-29- $FSLDIR/bin/avscale --allparams grot.mat $basenm | grep 'Translations' | sed 's/.* = //' >> ec_trans.txt ;
fsl-5.0.8/src/fdt/ec_plot:30: m=`echo $m + 1 | bc`;
fsl-5.0.8/src/fdt/ec_plot-31-done
##############################################
fsl-5.0.8/src/fdt/bedpostx_single_slice.sh-72-
fsl-5.0.8/src/fdt/bedpostx_single_slice.sh:73:slicezp=`${FSLDIR}/bin/zeropad $slice 4`
fsl-5.0.8/src/fdt/bedpostx_single_slice.sh-74-
##############################################
fsl-5.0.8/src/fdt/bedpostx_preproc.sh-72-
fsl-5.0.8/src/fdt/bedpostx_preproc.sh:73:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
fsl-5.0.8/src/fdt/bedpostx_preproc.sh-74- ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
##############################################
fsl-5.0.8/src/fdt/facalc-89-
fsl-5.0.8/src/fdt/facalc:90:if [ `${FSLDIR}/bin/imtest ${bn}_L1` -eq 0 -o `${FSLDIR}/bin/imtest ${bn}_L2` -eq 0 -o `${FSLDIR}/bin/imtest ${bn}_L3` -eq 0 ];
fsl-5.0.8/src/fdt/facalc-91-then echo "Not all eigenvalue images exist"
##############################################
fsl-5.0.8/src/fdt/maskdyads-76-
fsl-5.0.8/src/fdt/maskdyads:77:d=`$FSLDIR/bin/remove_ext $1`
fsl-5.0.8/src/fdt/maskdyads-78-f=$2
##############################################
fsl-5.0.8/src/fdt/ocmr_preproc-97-#tsize=`fslval big4D dim4`
fsl-5.0.8/src/fdt/ocmr_preproc:98:#tpts=`echo "10k $zsize $nslices /p "|dc -`
fsl-5.0.8/src/fdt/ocmr_preproc:99:#afterdot=`echo $tpts | awk -F . '{print \$2}'`
fsl-5.0.8/src/fdt/ocmr_preproc:100:#foo=`echo $afterdot|grep [123456798]`
fsl-5.0.8/src/fdt/ocmr_preproc-101-#if [ ! "$foo" = "" ]; then
##############################################
fsl-5.0.8/src/fdt/fdt_rotate_bvecs-42-
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:43: m11=`avscale $tmpo | grep Rotation -A 1 | tail -n 1| awk '{print $1}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:44: m12=`avscale $tmpo | grep Rotation -A 1 | tail -n 1| awk '{print $2}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:45: m13=`avscale $tmpo | grep Rotation -A 1 | tail -n 1| awk '{print $3}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:46: m21=`avscale $tmpo | grep Rotation -A 2 | tail -n 1| awk '{print $1}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:47: m22=`avscale $tmpo | grep Rotation -A 2 | tail -n 1| awk '{print $2}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:48: m23=`avscale $tmpo | grep Rotation -A 2 | tail -n 1| awk '{print $3}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:49: m31=`avscale $tmpo | grep Rotation -A 3 | tail -n 1| awk '{print $1}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:50: m32=`avscale $tmpo | grep Rotation -A 3 | tail -n 1| awk '{print $2}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:51: m33=`avscale $tmpo | grep Rotation -A 3 | tail -n 1| awk '{print $3}'`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs-52-
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:53: X=`cat $i | awk -v x=$ii '{print $x}' | head -n 1 | tail -n 1 | awk -F"E" 'BEGIN{OFMT="%10.10f"} {print $1 * (10 ^ $2)}' `
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:54: Y=`cat $i | awk -v x=$ii '{print $x}' | head -n 2 | tail -n 1 | awk -F"E" 'BEGIN{OFMT="%10.10f"} {print $1 * (10 ^ $2)}' `
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:55: Z=`cat $i | awk -v x=$ii '{print $x}' | head -n 3 | tail -n 1 | awk -F"E" 'BEGIN{OFMT="%10.10f"} {print $1 * (10 ^ $2)}' `
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:56: rX=`echo "scale=7; ($m11 * $X) + ($m12 * $Y) + ($m13 * $Z)" | bc -l`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:57: rY=`echo "scale=7; ($m21 * $X) + ($m22 * $Y) + ($m23 * $Z)" | bc -l`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs:58: rZ=`echo "scale=7; ($m31 * $X) + ($m32 * $Y) + ($m33 * $Z)" | bc -l`
fsl-5.0.8/src/fdt/fdt_rotate_bvecs-59-
##############################################
fsl-5.0.8/src/fdt/zeropad-83-
fsl-5.0.8/src/fdt/zeropad:84:i=`echo $1 | wc -c`;
fsl-5.0.8/src/fdt/zeropad-85-j=0;
fsl-5.0.8/src/fdt/zeropad:86:k=` expr $2 - $i`;
fsl-5.0.8/src/fdt/zeropad:87:k=` expr $k + 1`;
fsl-5.0.8/src/fdt/zeropad-88-num=$1;
##############################################
fsl-5.0.8/src/fdt/zeropad-90-num=0$num;
fsl-5.0.8/src/fdt/zeropad:91:j=` expr $j + 1`
fsl-5.0.8/src/fdt/zeropad-92-done
##############################################
fsl-5.0.8/src/fdt/bedpostx_datacheck-74-for img in ${DIR}/data ${DIR}/nodif_brain_mask ;do
fsl-5.0.8/src/fdt/bedpostx_datacheck:75: if [ `${FSLDIR}/bin/imtest $img` -eq 1 ] ; then
fsl-5.0.8/src/fdt/bedpostx_datacheck-76- echo $img
##############################################
fsl-5.0.8/src/fdt/bedpostx_datacheck-90-
fsl-5.0.8/src/fdt/bedpostx_datacheck:91:if [ `${FSLDIR}/bin/imtest ${DIR}/data` -eq 1 ] && [ `${FSLDIR}/bin/imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
fsl-5.0.8/src/fdt/bedpostx_datacheck-92-
fsl-5.0.8/src/fdt/bedpostx_datacheck:93: dx=`${FSLDIR}/bin/fslval ${DIR}/data dim1`
fsl-5.0.8/src/fdt/bedpostx_datacheck:94: dy=`${FSLDIR}/bin/fslval ${DIR}/data dim2`
fsl-5.0.8/src/fdt/bedpostx_datacheck:95: dz=`${FSLDIR}/bin/fslval ${DIR}/data dim3`
fsl-5.0.8/src/fdt/bedpostx_datacheck:96: dt=`${FSLDIR}/bin/fslval ${DIR}/data dim4`
fsl-5.0.8/src/fdt/bedpostx_datacheck-97-
fsl-5.0.8/src/fdt/bedpostx_datacheck:98: nbmx=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim1`
fsl-5.0.8/src/fdt/bedpostx_datacheck:99: nbmy=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim2`
fsl-5.0.8/src/fdt/bedpostx_datacheck:100: nbmz=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim3`
fsl-5.0.8/src/fdt/bedpostx_datacheck-101-
##############################################
fsl-5.0.8/src/fdt/bedpostx_datacheck-106-
fsl-5.0.8/src/fdt/bedpostx_datacheck:107: bvallenw=`cat ${DIR}/bvals|wc -w`
fsl-5.0.8/src/fdt/bedpostx_datacheck:108: bvallenl=`cat ${DIR}/bvals|grep -v "^[ ]*$"|wc -l`
fsl-5.0.8/src/fdt/bedpostx_datacheck:109: bvallen=`echo "$bvallenw / $bvallenl"|bc`
fsl-5.0.8/src/fdt/bedpostx_datacheck-110-
fsl-5.0.8/src/fdt/bedpostx_datacheck:111: bveclenw=`cat ${DIR}/bvecs|wc -w`
fsl-5.0.8/src/fdt/bedpostx_datacheck:112: bveclenl=`cat ${DIR}/bvecs|grep -v "^[ ]*$"|wc -l`
fsl-5.0.8/src/fdt/bedpostx_datacheck:113: bveclen=`echo "$bveclenw / $bveclenl"|bc`
fsl-5.0.8/src/fdt/bedpostx_datacheck-114-
##############################################
fsl-5.0.8/src/fdt/bedpostx-105- slice=0
fsl-5.0.8/src/fdt/bedpostx:106: errorFiles=\`ls ${subjdir}.bedpostX/logs/*.e* 2> /dev/null \`
fsl-5.0.8/src/fdt/bedpostx-107- for errorFile in \$errorFiles
##############################################
fsl-5.0.8/src/fdt/bedpostx-135- if [ "x$SGE_ROOT" = "x" ]; then
fsl-5.0.8/src/fdt/bedpostx:136: havedad=\`ps -e -o pid | grep "$$\\b" | wc -l\`
fsl-5.0.8/src/fdt/bedpostx-137- fi
##############################################
fsl-5.0.8/src/fdt/bedpostx-159-myopts="$@"
fsl-5.0.8/src/fdt/bedpostx:160:subjdir=`make_absolute $1`
fsl-5.0.8/src/fdt/bedpostx:161:subjdir=`echo $subjdir | sed 's/\/$/$/g'`
fsl-5.0.8/src/fdt/bedpostx-162-
##############################################
fsl-5.0.8/src/fdt/bedpostx-233-
fsl-5.0.8/src/fdt/bedpostx:234:if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
fsl-5.0.8/src/fdt/bedpostx-235- echo "${subjdir}/data not found"
##############################################
fsl-5.0.8/src/fdt/bedpostx-239-if [ ${gflag} -eq 1 ]; then
fsl-5.0.8/src/fdt/bedpostx:240: if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev` -eq 0 ]; then
fsl-5.0.8/src/fdt/bedpostx-241- echo "${subjdir}/grad_dev not found"
##############################################
fsl-5.0.8/src/fdt/bedpostx-245-
fsl-5.0.8/src/fdt/bedpostx:246:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
fsl-5.0.8/src/fdt/bedpostx-247- echo "${subjdir}/nodif_brain_mask not found"
##############################################
fsl-5.0.8/src/fdt/bedpostx-269-# don't setup email options, rely on fsl_sub's setting
fsl-5.0.8/src/fdt/bedpostx:270:#preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/src/fdt/bedpostx:271:preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/src/fdt/bedpostx-272-
fsl-5.0.8/src/fdt/bedpostx-273-echo Queuing parallel processing stage
fsl-5.0.8/src/fdt/bedpostx:274:nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
fsl-5.0.8/src/fdt/bedpostx-275-[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
##############################################
fsl-5.0.8/src/fdt/bedpostx-285-do
fsl-5.0.8/src/fdt/bedpostx:286: slicezp=`$FSLDIR/bin/zeropad $slice 4`
fsl-5.0.8/src/fdt/bedpostx:287: if [ `$FSLDIR/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ] && [ -f ${subjdir}.bedpostX/logs/monitor/$slice ];then
fsl-5.0.8/src/fdt/bedpostx-288- echo "slice $slice has already been processed"
##############################################
fsl-5.0.8/src/fdt/bedpostx-301-# don't specify a mailto address, but rely on fsl_sub doing it
fsl-5.0.8/src/fdt/bedpostx:302:bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
fsl-5.0.8/src/fdt/bedpostx-303-
##############################################
fsl-5.0.8/src/fdt/bedpostx-305-# don't setup email options, rely on fsl_sub's setting
fsl-5.0.8/src/fdt/bedpostx:306:mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
fsl-5.0.8/src/fdt/bedpostx-307-
##############################################
fsl-5.0.8/src/possum/generate_brain-85-
fsl-5.0.8/src/possum/generate_brain:86:struct=`remove_ext $1`
fsl-5.0.8/src/possum/generate_brain-87-
##############################################
fsl-5.0.8/src/possum/generate_b0-88-
fsl-5.0.8/src/possum/generate_b0:89:struct=`remove_ext $1`
fsl-5.0.8/src/possum/generate_b0:90:fmap=`remove_ext $2`
fsl-5.0.8/src/possum/generate_b0-91-TEdiff=$3
##############################################
fsl-5.0.8/src/possum/possumX_postproc.sh-110-if [ -e ${subjdir}/noise ]; then
fsl-5.0.8/src/possum/possumX_postproc.sh:111: n=`cat ${subjdir}/noise | awk '{print $1 }'`
fsl-5.0.8/src/possum/possumX_postproc.sh:112: m=`cat ${subjdir}/noise | awk '{print $2 }'`
fsl-5.0.8/src/possum/possumX_postproc.sh-113-fi
fsl-5.0.8/src/possum/possumX_postproc.sh-114-
fsl-5.0.8/src/possum/possumX_postproc.sh:115:if [ `${FSLDIR}/bin/imtest ${subjdir}/image_homo` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX_postproc.sh-116- imcp image_homo image_abs
##############################################
fsl-5.0.8/src/possum/possumX_postproc.sh-119-fslmaths ${subjdir}/image_abs -Tmean ${subjdir}/image_mean
fsl-5.0.8/src/possum/possumX_postproc.sh:120:P98=`fslstats ${subjdir}/image_mean -P 98`
fsl-5.0.8/src/possum/possumX_postproc.sh:121:P02=`fslstats ${subjdir}/image_mean -P 2`
fsl-5.0.8/src/possum/possumX_postproc.sh:122:tresh=`echo "0.1 * $P98 + 0.9 * $P02 "|bc -l`
fsl-5.0.8/src/possum/possumX_postproc.sh-123-fslmaths ${subjdir}/image_mean -thr $tresh ${subjdir}/image_mean
fsl-5.0.8/src/possum/possumX_postproc.sh:124:medint=`fslstats ${subjdir}/image_mean -P 50`
fsl-5.0.8/src/possum/possumX_postproc.sh:125:dim1=`fslval ${subjdir}/image_abs dim1`
fsl-5.0.8/src/possum/possumX_postproc.sh-126-if [ $n = "snr" ]; then
##############################################
fsl-5.0.8/src/possum/possumX_postproc.sh-128- if [ $snr != 0 ]; then
fsl-5.0.8/src/possum/possumX_postproc.sh:129: #sigma=`echo " ${medint} / ( 2 * ${dim1} * ${snr} ) "| bc -l` #I worked this out ages ago.
fsl-5.0.8/src/possum/possumX_postproc.sh:130: sigma=`echo " ${medint} / $snr " | bc -l`
fsl-5.0.8/src/possum/possumX_postproc.sh-131- echo "sigma ${sigma} snr ${snr} medintensity ${medint}" > ${subjdir}/noise
##############################################
fsl-5.0.8/src/possum/possumX_postproc.sh-137- if [ $sigma != 0 ]; then
fsl-5.0.8/src/possum/possumX_postproc.sh:138: snr=`echo " ${medint} / ( 2 * ${dim1} * ${sigma} ) "| bc -l`
fsl-5.0.8/src/possum/possumX_postproc.sh-139- echo "sigma $sigma snr $snr" > ${subjdir}/noise
##############################################
fsl-5.0.8/src/possum/possumX_postproc.sh-143- mv ${subjdir}/signal ${subjdir}/signal_nonoise
fsl-5.0.8/src/possum/possumX_postproc.sh:144: sigma=`echo "${sigma} / ${dim1} " | bc -l `
fsl-5.0.8/src/possum/possumX_postproc.sh-145- echo sigma for system noise is $sigma
##############################################
fsl-5.0.8/src/possum/possumX_postproc.sh-150-
fsl-5.0.8/src/possum/possumX_postproc.sh:151:if [ `${FSLDIR}/bin/imtest ${subjdir}/image_homo` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX_postproc.sh-152- imrm image_abs
##############################################
fsl-5.0.8/src/possum/possumX-140-
fsl-5.0.8/src/possum/possumX:141:subjdir=`make_absolute $1`
fsl-5.0.8/src/possum/possumX-142-# tejas-edit 05.11.12
fsl-5.0.8/src/possum/possumX:143:subjdir=`echo $subjdir | sed 's/\/$/$/g'` 1>/dev/null
fsl-5.0.8/src/possum/possumX-144-# tejas-end
##############################################
fsl-5.0.8/src/possum/possumX-191-
fsl-5.0.8/src/possum/possumX:192:if [ `${FSLDIR}/bin/imtest ${subjdir}/brain` -eq 0 ]; then
fsl-5.0.8/src/possum/possumX:193: if [ `${FSLDIR}/bin/imtest ${subjdir}/object` -eq 0 ]; then
fsl-5.0.8/src/possum/possumX-194- echo "could not find ${subjdir}/brain or ${subjdir}/object"
##############################################
fsl-5.0.8/src/possum/possumX-204-
fsl-5.0.8/src/possum/possumX:205:if [ `${FSLDIR}/bin/imtest ${subjdir}/RFtrans` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX-206- command="$command -s ${subjdir}/RFtrans"
##############################################
fsl-5.0.8/src/possum/possumX-208-
fsl-5.0.8/src/possum/possumX:209:if [ `${FSLDIR}/bin/imtest ${subjdir}/RFrec` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX-210- command="$command -r ${subjdir}/RFrec"
##############################################
fsl-5.0.8/src/possum/possumX-212-
fsl-5.0.8/src/possum/possumX:213:if [ `${FSLDIR}/bin/imtest ${subjdir}/T2` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX-214- command="$command -a ${subjdir}/T2 -t ${subjdir}/T2timecourse"
##############################################
fsl-5.0.8/src/possum/possumX-219-
fsl-5.0.8/src/possum/possumX:220:if [ `${FSLDIR}/bin/imtest ${subjdir}/T2_4D` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX-221- command="$command -q ${subjdir}/T2_4D -u ${subjdir}/T2_4Dtimecourse"
##############################################
fsl-5.0.8/src/possum/possumX-226-
fsl-5.0.8/src/possum/possumX:227:if [ `${FSLDIR}/bin/imtest ${subjdir}/b0z_dz` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX-228- command="$command -b ${subjdir}/b0"
##############################################
fsl-5.0.8/src/possum/possumX-230-
fsl-5.0.8/src/possum/possumX:231:if [ `${FSLDIR}/bin/imtest ${subjdir}/b0extra` -eq 1 ]; then
fsl-5.0.8/src/possum/possumX-232- command="$command --b0extra=${subjdir}/b0extra --b0time=${subjdir}/b0timecourse -l 4"
##############################################
fsl-5.0.8/src/possum/possumX-281-unset LD_LIBRARY_PATH DYLD_LIBRARY_PATH DYLD_FALLBACK_LIBRARY_PATH
fsl-5.0.8/src/possum/possumX:282:possumid=`${FSLDIR}/bin/fsl_sub -T $ntime ${hold}-l ${subjdir}/logs $arch -N possum -t ${subjdir}/possum.com`
fsl-5.0.8/src/possum/possumX-283-#tejas-end
##############################################
fsl-5.0.8/src/possum/possumX-290-
fsl-5.0.8/src/possum/possumX:291:mergeid=`${FSLDIR}/bin/fsl_sub -T 10 -j $possumid -F -l ${subjdir}/logs $arch ${POSSUMDIR}/bin/possumX_postproc.sh $subjdir $nproc`
fsl-5.0.8/src/possum/possumX-292-
##############################################
fsl-5.0.8/config/common/buildproj-16-FSLCONFDIR=${FSLDIR}/config
fsl-5.0.8/config/common/buildproj:17:FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
fsl-5.0.8/config/common/buildproj-18-export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE
##############################################
fsl-5.0.8/config/common/insertcopyright-16- # Insert CCOPYRIGHT message
fsl-5.0.8/config/common/insertcopyright:17: num=`grep -n CCOPYRIGHT $fname | head -1 | cut -d':' -f1 `; export num
fsl-5.0.8/config/common/insertcopyright-18- if [ "X${num}X" != XX ] ; then
fsl-5.0.8/config/common/insertcopyright:19: num1=`echo "$num 1 - p" | dc`; export num1
fsl-5.0.8/config/common/insertcopyright-20- com1="1,${num1}p"; export com1
fsl-5.0.8/config/common/insertcopyright:21: num2=`echo "$num 1 + p" | dc`; export num2
fsl-5.0.8/config/common/insertcopyright-22- com2="${num2},\$p"; export com2
##############################################
fsl-5.0.8/config/common/insertcopyright-31- # Insert TCLCOPYRIGHT message
fsl-5.0.8/config/common/insertcopyright:32: num=`grep -n TCLCOPYRIGHT $fname | head -1 | cut -d':' -f1 `; export num
fsl-5.0.8/config/common/insertcopyright-33- if [ "X${num}X" != XX ] ; then
fsl-5.0.8/config/common/insertcopyright:34: num1=`echo "$num 1 - p" | dc`; export num1
fsl-5.0.8/config/common/insertcopyright-35- com1="1,${num1}p"; export com1
fsl-5.0.8/config/common/insertcopyright:36: num2=`echo "$num 1 + p" | dc`; export num2
fsl-5.0.8/config/common/insertcopyright-37- com2="${num2},\$p"; export com2
##############################################
fsl-5.0.8/config/common/insertcopyright-46- # Insert SHCOPYRIGHT message
fsl-5.0.8/config/common/insertcopyright:47: num=`grep -n SHCOPYRIGHT $fname | head -1 | cut -d':' -f1 `; export num
fsl-5.0.8/config/common/insertcopyright-48- if [ "X${num}X" != XX ] ; then
fsl-5.0.8/config/common/insertcopyright:49: num1=`echo "$num 1 - p" | dc`; export num1
fsl-5.0.8/config/common/insertcopyright-50- com1="1,${num1}p"; export com1
fsl-5.0.8/config/common/insertcopyright:51: num2=`echo "$num 1 + p" | dc`; export num2
fsl-5.0.8/config/common/insertcopyright-52- com2="${num2},\$p"; export com2
##############################################
fsl-5.0.8/config/common/insertcopyright-62- # Insert SHBASECOPYRIGHT message
fsl-5.0.8/config/common/insertcopyright:63: num=`grep -n SHBASECOPYRIGHT $fname | head -1 | cut -d':' -f1 `; export num
fsl-5.0.8/config/common/insertcopyright-64- if [ "X${num}X" != XX ] ; then
fsl-5.0.8/config/common/insertcopyright:65: num1=`echo "$num 1 - p" | dc`; export num1
fsl-5.0.8/config/common/insertcopyright-66- com1="1,${num1}p"; export com1
fsl-5.0.8/config/common/insertcopyright:67: num2=`echo "$num 1 + p" | dc`; export num2
fsl-5.0.8/config/common/insertcopyright-68- com2="${num2},\$p"; export com2
##############################################
fsl-5.0.8/etc/fslconf/fsl.sh-52-#FSLCONFDIR=$FSLDIR/config
fsl-5.0.8/etc/fslconf/fsl.sh:53:#FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
fsl-5.0.8/etc/fslconf/fsl.sh-54-
##############################################
fsl-5.0.8/etc/fslconf/fslmachtype.sh-26- # GCC is installed
fsl-5.0.8/etc/fslconf/fslmachtype.sh:27: gcc_version=`echo $gcc_version | $AWK -F . '{ printf "%s.%s", $1,$2 }'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh-28- gcc_host=`gcc -dumpmachine`
fsl-5.0.8/etc/fslconf/fslmachtype.sh-29-
fsl-5.0.8/etc/fslconf/fslmachtype.sh:30: gcc_cpu_type=`echo $gcc_host | $AWK -F - '{ printf "%s", $1; }'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh:31: gcc_os_vendor=`echo $gcc_host | $AWK -F - '{ printf "%s", $2; }'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh:32: gcc_os_name=`echo $gcc_host | $AWK -F - '{ printf "%s", $3; }'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh-33-
##############################################
fsl-5.0.8/etc/fslconf/fslmachtype.sh-37- # combined binary, so we only need 1 host type
fsl-5.0.8/etc/fslconf/fslmachtype.sh:38: os_release=`uname -r | $AWK -F . '{ printf "%s", $1 }'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh-39- if [ $os_release -ge 12 ]; then
##############################################
fsl-5.0.8/etc/fslconf/fslmachtype.sh-41- llvm_vstr=`cc -v 2>&1`
fsl-5.0.8/etc/fslconf/fslmachtype.sh:42: llvm_v=`echo ${llvm_vstr} | awk '{ print $4 }'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh:43: os_v=`echo ${llvm_vstr} | awk '{ print $11 }' | awk -F. '{ print $1 }' | sed 's/x86_64-//'`
fsl-5.0.8/etc/fslconf/fslmachtype.sh-44- machtype=${os_v}-llvm${llvm_v}
##############################################
fsl-5.0.8/etc/fslconf/fslmachtype.sh-59- gcc_host="${gcc_os_name}_64"
fsl-5.0.8/etc/fslconf/fslmachtype.sh:60: elif [ `echo ${gcc_cpu_type} | grep i.86` ]; then
fsl-5.0.8/etc/fslconf/fslmachtype.sh-61- gcc_host="${gcc_os_name}_32"
##############################################
fsl-5.0.8/etc/fslconf/fsl-devel.sh-52-FSLCONFDIR=$FSLDIR/config
fsl-5.0.8/etc/fslconf/fsl-devel.sh:53:FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
fsl-5.0.8/etc/fslconf/fsl-devel.sh-54-
##############################################
fsl-5.0.8/etc/fslconf/fsl.csh-45-#setenv FSLCONFDIR $FSLDIR/config
fsl-5.0.8/etc/fslconf/fsl.csh:46:#setenv FSLMACHTYPE `$FSLDIR/etc/fslconf/fslmachtype.sh`
fsl-5.0.8/etc/fslconf/fsl.csh-47-
##############################################
fsl-5.0.8/extras/build-20-if [ -z "$FSLMACHTYPE" ]; then
fsl-5.0.8/extras/build:21: FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
fsl-5.0.8/extras/build-22-fi
##############################################
fsl-5.0.8/extras/build-48- # Are we running on a Mac Pre 10.8?
fsl-5.0.8/extras/build:49: MAC_V=`uname -r | awk -F. '{ print $1 }'`
fsl-5.0.8/extras/build-50- if [ ${MAC_V} -lt 12 ]; then
##############################################
fsl-5.0.8/debian/fsl-core.preinst-14- if [ -e "$CONFFILE" ]; then
fsl-5.0.8/debian/fsl-core.preinst:15: md5sum="`md5sum \"$CONFFILE\" | sed -e \"s/ .*//\"`"
fsl-5.0.8/debian/fsl-core.preinst-16- old_md5sum=$(dpkg-query -W -f='${Conffiles}' fsl | grep ${CONFFILE} | awk '{ print $2 }')
##############################################
fsl-5.0.8/debian/patches/debian_sge-15- echo Queuing preprocessing stages
fsl-5.0.8/debian/patches/debian_sge:16:-preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/debian/patches/debian_sge-17-+# don't setup email options, rely on fsl_sub's setting
fsl-5.0.8/debian/patches/debian_sge:18:+#preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/debian/patches/debian_sge:19:+preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/debian/patches/debian_sge-20-
fsl-5.0.8/debian/patches/debian_sge-21- echo Queuing parallel processing stage
fsl-5.0.8/debian/patches/debian_sge:22: nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
fsl-5.0.8/debian/patches/debian_sge-23- [ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
##############################################
fsl-5.0.8/debian/patches/debian_sge-35- done
fsl-5.0.8/debian/patches/debian_sge:36:-bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
fsl-5.0.8/debian/patches/debian_sge-37-+# don't specify a mailto address, but rely on fsl_sub doing it
fsl-5.0.8/debian/patches/debian_sge:38:+bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
fsl-5.0.8/debian/patches/debian_sge-39-
fsl-5.0.8/debian/patches/debian_sge-40- echo Queuing post processing stage
fsl-5.0.8/debian/patches/debian_sge:41:-mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
fsl-5.0.8/debian/patches/debian_sge-42-+# don't setup email options, rely on fsl_sub's setting
fsl-5.0.8/debian/patches/debian_sge:43:+mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
fsl-5.0.8/debian/patches/debian_sge-44-
##############################################
fsl-5.0.8/debian/patches/debian_sge-116- unset LD_LIBRARY_PATH DYLD_LIBRARY_PATH DYLD_FALLBACK_LIBRARY_PATH
fsl-5.0.8/debian/patches/debian_sge:117:-possumid=`${FSLDIR}/bin/fsl_sub -T $ntime ${hold}-l ${subjdir}/logs $arch -M $mailto -N possum -t ${subjdir}/possum.com`
fsl-5.0.8/debian/patches/debian_sge:118:+possumid=`${FSLDIR}/bin/fsl_sub -T $ntime ${hold}-l ${subjdir}/logs $arch -N possum -t ${subjdir}/possum.com`
fsl-5.0.8/debian/patches/debian_sge-119- #tejas-end
##############################################
fsl-5.0.8/debian/patches/fix_bashisms-58-+ if [ "x$SGE_ROOT" = "x" ]; then
fsl-5.0.8/debian/patches/fix_bashisms:59: havedad=\`ps -e -o pid | grep "$$\\b" | wc -l\`
fsl-5.0.8/debian/patches/fix_bashisms-60- fi
##############################################
fsl-5.0.8/debian/templates/meta.preinst-14- if [ -e "$CONFFILE" ]; then
fsl-5.0.8/debian/templates/meta.preinst:15: md5sum="`md5sum \"$CONFFILE\" | sed -e \"s/ .*//\"`"
fsl-5.0.8/debian/templates/meta.preinst-16- old_md5sum=$(dpkg-query -W -f='${Conffiles}' fsl | grep ${CONFFILE} | awk '{ print $2 }')
##############################################
fsl-5.0.8/debian/tests/fnirt_noaffine_bug.sh-63-
fsl-5.0.8/debian/tests/fnirt_noaffine_bug.sh:64:[ 1 -eq `echo "$MSENLIN2 > $MSENLIN2b * 100" | bc` ] && { echo; echo "*** FOUND FNIRT BUG ***"; exit 17; }
fsl-5.0.8/debian/tests/fnirt_noaffine_bug.sh-65-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-167- outdir=$outdir"+"
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:168: count=`expr $count + 1`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-169-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-181-# make a temp directory to work in
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:182:tmpbase=`$FSLDIR/bin/tmpnam`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-183-tempdir=${tmpbase}_quasil
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-193-tislist=""
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:194:thetis=`echo $tis | sed 's:,: :g'`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-195-for ti in $thetis; do
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:196: count=`expr ${count} + 1`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:197: tislist=`echo $tislist --ti${count}=$ti`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-198-done
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-250- mkdir ti$i
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:251: tifile=`ls ti$i.nii.gz ti0$i.nii.gz ti00$i.nii.gz 2>/dev/null`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-252- echo $tifile
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-282-# we do not (currently) use this for the main analysis
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:283:nkeep=`expr $ntis \* 6`
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-284-fslroi asldata asldata 0 $nkeep
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-334- #fslmaths instruction for calibration (for execution whilst back in starting dir)
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil:335: cinstr=" -div `cat $tempdir/calib/M0a.txt` "
fsl-5.0.8/.pc/fix_bashisms/src/oxford_asl/quasil-336-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-47-[ "$2" = "" ] && usage
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:48:[ `${FSLDIR}/bin/imtest $1` = 0 ] && usage
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:49:[ `${FSLDIR}/bin/imtest $2` = 0 ] && usage
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:50:[ `${FSLDIR}/bin/imtest $3` = 0 ] && usage
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-51-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-107-do
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:108: if [ `${FSLDIR}/bin/imtest $VOL` = 0 ] ; then
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-109- echo "Error, file does not exist: $VOL" >> $LOG
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-124-${FSLDIR}/bin/fslmaths ${scbaseflow} -mas ${scbasehalf}_ventricle_region_bin ${scbaseflow}_ventricles
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:125:edgepointsbase=`${FSLDIR}/bin/fslstats ${scbaseedge}_ventricles -V | cut -d' ' -f1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:126:infobaseflow=`${FSLDIR}/bin/fslstats ${scbaseflow}_ventricles -V -M`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:127:nonzeroflowbase=`echo ${infobaseflow} | cut -d' ' -f1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:128:tempmeanflowbase=`echo ${infobaseflow} | cut -d' ' -f3`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:129:meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-130-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-131-# Determine only one of three pixdims because we have isotropic pixels.
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:132:pixdimbase=`${FSLDIR}/bin/fslval ${scbasehalf} pixdim1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-133-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-134-# Calculate PVVC
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:135:temppvvcbase=`echo "10 k 30 ${pixdimbase} * ${meanflowbase} * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-136-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-137-# We assume standard FSL settings have been used, i.e. 0.2% change for calibration, change above if not true.
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:138:vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:139:calibbase=`echo "10 k ${vm} ${temppvvcbase} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-140-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-157-${FSLDIR}/bin/fslmaths ${scfollowflow} -mas ${scfollowhalf}_ventricle_region_bin ${scfollowflow}_ventricles
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:158:edgepointsfollow=`${FSLDIR}/bin/fslstats ${scfollowedge}_ventricles -V|cut -f 1 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:159:infofollowflow=`${FSLDIR}/bin/fslstats ${scfollowflow}_ventricles -V -M`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:160:nonzeroflowfollow=`echo ${infofollowflow} | cut -d' ' -f1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:161:tempmeanflowfollow=`echo ${infofollowflow} | cut -d' ' -f3`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:162:meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-163-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-164-# Determine only one of three pixdims because we have isotropic pixels.
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:165:pixdimfollow=`${FSLDIR}/bin/fslval ${scfollowhalf} pixdim1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-166-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-167-# Calculate PVVC
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:168:temppvvcfollow=`echo "10 k 30 ${pixdimfollow} * ${meanflowfollow} * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-169-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-170-# We assume standard FSL settings have been used, i.e. 0.2% change for calibration, change above if not true.
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:171:vm=`echo "10 k ${m} 6 ^ 1.0 - 100.0 * p" | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:172:calibfollow=`echo "10 k ${vm} ${temppvvcfollow} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-173-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-205-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:206:edgepointsbase=`${FSLDIR}/bin/fslstats ${base}_to_${follow}_edgepoints_ventricles -V|cut -f 1 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:207:infobaseflow=`${FSLDIR}/bin/fslstats ${base}_to_${follow}_flow_ventricles -V -M`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:208:nonzeroflowbase=`echo ${infobaseflow}|cut -f 1 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:209:tempmeanflowbase=`echo ${infobaseflow}|cut -f 3 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:210:meanflowbase=`echo "10 k ${tempmeanflowbase} ${nonzeroflowbase} * ${edgepointsbase} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:211:pixdimbase=`${FSLDIR}/bin/fslval ${base}_halfwayto_${follow} pixdim1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-212-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:213:edgepointsfollow=`${FSLDIR}/bin/fslstats ${follow}_to_${base}_edgepoints_ventricles -V|cut -f 1 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:214:infofollowflow=`${FSLDIR}/bin/fslstats ${follow}_to_${base}_flow_ventricles -V -M`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:215:nonzeroflowfollow=`echo ${infofollowflow} | cut -f 1 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:216:tempmeanflowfollow=`echo ${infofollowflow} | cut -f 3 -d " "`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:217:meanflowfollow=`echo "10 k ${tempmeanflowfollow} ${nonzeroflowfollow} * ${edgepointsfollow} / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:218:pixdimfollow=`${FSLDIR}/bin/fslval ${follow}_halfwayto_${base} pixdim1`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-219-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-220-# Calculate PVVC base -> follow
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:221:pvvcbasetofollow=`echo "10 k 30 ${calibbase} * ${pixdimbase} * ${meanflowbase} * _1.0 * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-222-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-223-# Calculate PVVC follow -> base
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:224:pvvcfollowtobase=`echo "10 k 30 ${calibfollow} * ${pixdimfollow} * ${meanflowfollow} * _1.0 * p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:225:denom=`echo "10 k ${pvvcfollowtobase} 100 / 1.0 + p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:226:tmpbackwards=`echo "10 k ${pvvcfollowtobase} ${denom} / _1.0 * p" |sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-227-
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant:228:meanpvvc=`echo "10 k ${pvvcbasetofollow} ${tmpbackwards} + 2 / p" | sed 's/-/_/g' | dc -`
fsl-5.0.8/.pc/fix_bashisms/src/siena/viena_quant-229-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-84-for d in $@ ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:85: cnt=`echo "$cnt+1" | bc -l`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-86-done
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-114- echo $m
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:115: for f in `$FSLDIR/bin/imglob *` ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:116: ff=`$FSLDIR/bin/remove_ext $f`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-117- echo $ff
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-132- echo $m
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:133: for f in `$FSLDIR/bin/imglob *` ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:134: ff=`$FSLDIR/bin/remove_ext $f`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-135- echo $ff
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-155- echo $m
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:156: $FSLDIR/bin/fslmerge -t ../stats/all_${m} `$FSLDIR/bin/imglob *_to_target_${m}.*`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-157- $FSLDIR/bin/fslmaths ../stats/all_${m} -mas ../stats/mean_FA_mask ../stats/all_${m}
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-162- for xyz in x y z;do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:163: for f in `$FSLDIR/bin/imglob *_to_target_${m}.*` ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-164- echo $f
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:165: fslroi ${f} `$FSLDIR/bin/remove_ext ${f}`_${xyz} ${i} 1
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-166- done
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:167: $FSLDIR/bin/fslmerge -t ../stats/all_${m}_${xyz} `$FSLDIR/bin/imglob *_to_target_${m}_${xyz}.*`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-168- $FSLDIR/bin/fslmaths ../stats/all_${m}_${xyz} -mas ../stats/mean_FA_mask ../stats/all_${m}_${xyz}
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:169: $FSLDIR/bin/imrm `$FSLDIR/bin/imglob *_to_target_${m}_${xyz}.*`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-170- let "i+=1"
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-203- $FSLDIR/bin/fslsplit all_${m}_skeletonised all_${m}_skeletonised_
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:204: for im in `$FSLDIR/bin/imglob all_${m}_skeletonised_????.*` ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:205: n=`echo $im | sed s/all_"${m}"_skeletonised_//g`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-206- echo $im >> .scalist${n}.txt
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-214- done
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:215: for im in `$FSLDIR/bin/imglob all_${m}_x_skeletonised_????.*` ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:216: n=`echo $im | sed s/all_"${m}"_x_skeletonised_//g`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-217- $FSLDIR/bin/fslmerge -t all_${m}_skeletonised_$n all_${m}_x_skeletonised_$n all_${m}_y_skeletonised_$n all_${m}_z_skeletonised_$n
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-228-for list in .scalist????.txt ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:229: n=`echo $list | sed s/.scalist//g | sed s/.txt//g`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-230- subjscalist=.scalist${n}.txt
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-233- fslmaths mean_FA_skeleton_mask mfibresmask
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:234: for f in `cat $subjscalist` ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-235- fslmaths $f -thr .1 -bin -mas mfibresmask mfibresmask
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-257-for i in .scalist????.txt ; do
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x:258: n=`echo $i | sed s/.scalist//g | sed s/.txt//g`
fsl-5.0.8/.pc/fix_bashisms/src/tbss/tbss_x-259- mm=1
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-76-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:77:RANDOMISE_OUTPUT=`$FSLDIR/bin/randomise $@ -Q`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-78-if [ $? != 0 ] ; then
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-82-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:83:PERMS=`echo $RANDOMISE_OUTPUT | awk '{print $1}'`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:84:CONTRASTS=`echo $RANDOMISE_OUTPUT | awk '{print $2}'`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:85:ROOTNAME=`echo $RANDOMISE_OUTPUT | awk '{print $3}'`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:86:BASENAME=`basename $ROOTNAME`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:87:DIRNAME=`dirname $ROOTNAME`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-88-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-90-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:91:PERMS_PER_SLOT=`echo $RANDOMISE_OUTPUT | awk '{print $4}'`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-92-if [ x${REQUESTED_TIME} = 'x' ] ; then
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-95-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:96:SLOTS_PER_CONTRAST=`expr $PERMS / $PERMS_PER_SLOT`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-97-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-101-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:102:PERMS_PER_CONTRAST=`expr $PERMS_PER_SLOT \* $SLOTS_PER_CONTRAST`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-103-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:104:REQUESTED_SLOTS=`expr $CONTRASTS \* $SLOTS_PER_CONTRAST`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-105-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:106:CORRECTED_PERMS=`expr $PERMS_PER_CONTRAST - $SLOTS_PER_CONTRAST`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:107:CORRECTED_PERMS=`expr $CORRECTED_PERMS + 1`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-108-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-117-while [ $CURRENT_SEED -le $SLOTS_PER_CONTRAST ] ; do
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:118: SLEEPTIME=`expr 1 \* $CURRENT_SEED`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-119- CURRENT_CONTRAST=1
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-121- echo "FSLOUTPUTTYPE=NIFTI_GZ; sleep $SLEEPTIME ; ${FSLDIR}/bin/randomise $@ -n $PERMS_PER_SLOT -o ${ROOTNAME}_SEED${CURRENT_SEED} --seed=$CURRENT_SEED --skipTo=$CURRENT_CONTRAST" >> ${DIRNAME}/${BASENAME}.generate
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:122: CURRENT_CONTRAST=`expr $CURRENT_CONTRAST + 1`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-123- done
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-124- echo done $CURRENT_SEED
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:125: CURRENT_SEED=`expr $CURRENT_SEED + 1`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-126-done
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-127-chmod a+x ${DIRNAME}/${BASENAME}.generate
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:128:GENERATE_ID=`$FSLDIR/bin/fsl_sub -T ${REQUESTED_TIME} -N ${BASENAME}.generate -l ${DIRNAME}/${BASENAME}_logs/ -t ${DIRNAME}/${BASENAME}.generate`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-129-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-138- while [ \$ACTIVESEED -le $SLOTS_PER_CONTRAST ] ; do
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:139: ADDCOMMAND=\`echo \$ADDCOMMAND -add \${FIRSTSEED/_SEED1_/_SEED\${ACTIVESEED}_}\`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:140: ACTIVESEED=\`expr \$ACTIVESEED + 1\`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-141- done
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-157- fi
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:158: ACTIVESEED=\`expr \$ACTIVESEED + 1\`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-159- done
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-181-
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel:182: ACTIVESEED=\`expr \$ACTIVESEED + 1\`
fsl-5.0.8/.pc/fix_bashisms/src/randomise/randomise_parallel-183-done
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-105- slice=0
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:106: errorFiles=\`ls ${subjdir}.bedpostX/logs/*.e* 2> /dev/null \`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-107- for errorFile in \$errorFiles
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-135- if [ "x$SGE_ROOT" == "x" ]; then
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:136: havedad=\`ps -e -o pid | grep "$$\\b" | wc -l\`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-137- fi
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-159-myopts="$@"
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:160:subjdir=`make_absolute $1`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:161:subjdir=`echo $subjdir | sed 's/\/$/$/g'`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-162-
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-233-
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:234:if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-235- echo "${subjdir}/data not found"
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-239-if [ ${gflag} -eq 1 ]; then
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:240: if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev` -eq 0 ]; then
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-241- echo "${subjdir}/grad_dev not found"
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-245-
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:246:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-247- echo "${subjdir}/nodif_brain_mask not found"
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-266-echo Queuing preprocessing stages
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:267:preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-268-
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-269-echo Queuing parallel processing stage
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:270:nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-271-[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-280-do
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:281: slicezp=`$FSLDIR/bin/zeropad $slice 4`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:282: if [ `$FSLDIR/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ] && [ -f ${subjdir}.bedpostX/logs/monitor/$slice ];then
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-283- echo "slice $slice has already been processed"
##############################################
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-295-done
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:296:bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-297-
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-298-echo Queuing post processing stage
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx:299:mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
fsl-5.0.8/.pc/fix_bashisms/src/fdt/bedpostx-300-
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-105- slice=0
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:106: errorFiles=\`ls ${subjdir}.bedpostX/logs/*.e* 2> /dev/null \`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-107- for errorFile in \$errorFiles
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-135- if [ "x$SGE_ROOT" = "x" ]; then
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:136: havedad=\`ps -e -o pid | grep "$$\\b" | wc -l\`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-137- fi
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-159-myopts="$@"
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:160:subjdir=`make_absolute $1`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:161:subjdir=`echo $subjdir | sed 's/\/$/$/g'`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-162-
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-233-
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:234:if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-235- echo "${subjdir}/data not found"
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-239-if [ ${gflag} -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:240: if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev` -eq 0 ]; then
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-241- echo "${subjdir}/grad_dev not found"
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-245-
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:246:if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-247- echo "${subjdir}/nodif_brain_mask not found"
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-266-echo Queuing preprocessing stages
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:267:preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-268-
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-269-echo Queuing parallel processing stage
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:270:nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-271-[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-280-do
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:281: slicezp=`$FSLDIR/bin/zeropad $slice 4`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:282: if [ `$FSLDIR/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ] && [ -f ${subjdir}.bedpostX/logs/monitor/$slice ];then
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-283- echo "slice $slice has already been processed"
##############################################
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-295-done
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:296:bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-297-
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-298-echo Queuing post processing stage
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx:299:mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
fsl-5.0.8/.pc/debian_sge/src/fdt/bedpostx-300-
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-140-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:141:subjdir=`make_absolute $1`
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-142-# tejas-edit 05.11.12
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:143:subjdir=`echo $subjdir | sed 's/\/$/$/g'` 1>/dev/null
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-144-# tejas-end
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-191-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:192:if [ `${FSLDIR}/bin/imtest ${subjdir}/brain` -eq 0 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:193: if [ `${FSLDIR}/bin/imtest ${subjdir}/object` -eq 0 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-194- echo "could not find ${subjdir}/brain or ${subjdir}/object"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-204-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:205:if [ `${FSLDIR}/bin/imtest ${subjdir}/RFtrans` -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-206- command="$command -s ${subjdir}/RFtrans"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-208-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:209:if [ `${FSLDIR}/bin/imtest ${subjdir}/RFrec` -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-210- command="$command -r ${subjdir}/RFrec"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-212-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:213:if [ `${FSLDIR}/bin/imtest ${subjdir}/T2` -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-214- command="$command -a ${subjdir}/T2 -t ${subjdir}/T2timecourse"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-219-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:220:if [ `${FSLDIR}/bin/imtest ${subjdir}/T2_4D` -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-221- command="$command -q ${subjdir}/T2_4D -u ${subjdir}/T2_4Dtimecourse"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-226-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:227:if [ `${FSLDIR}/bin/imtest ${subjdir}/b0z_dz` -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-228- command="$command -b ${subjdir}/b0"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-230-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:231:if [ `${FSLDIR}/bin/imtest ${subjdir}/b0extra` -eq 1 ]; then
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-232- command="$command --b0extra=${subjdir}/b0extra --b0time=${subjdir}/b0timecourse -l 4"
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-278-unset LD_LIBRARY_PATH DYLD_LIBRARY_PATH DYLD_FALLBACK_LIBRARY_PATH
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:279:possumid=`${FSLDIR}/bin/fsl_sub -T $ntime ${hold}-l ${subjdir}/logs $arch -M $mailto -N possum -t ${subjdir}/possum.com`
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-280-#tejas-end
##############################################
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-287-
fsl-5.0.8/.pc/debian_sge/src/possum/possumX:288:mergeid=`${FSLDIR}/bin/fsl_sub -T 10 -j $possumid -F -l ${subjdir}/logs $arch ${POSSUMDIR}/bin/possumX_postproc.sh $subjdir $nproc`
fsl-5.0.8/.pc/debian_sge/src/possum/possumX-289-
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-139-export POSIXLY_CORRECT
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:140:command=`basename $0`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-141-
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-196-
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:197:set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-198-result=$?
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-267- -z)
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:268: if [ -e $2 -o `${FSLDIR}/bin/imtest $2` = 1 ] ; then
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-269- exit 0
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-285- acceptable_arch=no
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:286: available_archs=`qhost | tail -n +4 | awk '{print $2}' | sort | uniq`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-287- for a in $available_archs; do
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-312- if [ -f "$taskfile" ] ; then
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:313: tasks=`wc -l $taskfile | awk '{print $1}'`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-314- if [ $tasks -ne 0 ]; then
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-352- pe_string=$2;
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:353: peName=`echo $pe_string | cut -d',' -f 1`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:354: peThreads=`echo $pe_string | cut -d',' -f 2`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-355- shift;;
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-379- if [ "x$taskfile" != x ] ; then
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:380: JobName=`basename $taskfile`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-381- else
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:382: JobName=`basename $1`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-383- fi
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-469-
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:470:command=\`sed -n -e "\${SGE_TASK_ID}p" $taskfile\`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-471-
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-502- while [ $n -le $tasks ] ; do
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:503: line=`sed -n -e ''${n}'p' $taskfile`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-504- if [ $verbose -eq 1 ] ; then
##############################################
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-509-EOF2
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub:510: n=`expr $n + 1`
fsl-5.0.8/.pc/debian_sge/src/sgeutils/fsl_sub-511- done