Commit 92d19c0f authored by Shaun Warrington's avatar Shaun Warrington
Browse files

Merge branch 'patch-191119' into 'master'

Patch 191119

See merge request !6
parents e20653fa dfac9802
## XTRACT - a command-line tool for automated tractography ## XTRACT - a command-line tool for automated tractography
XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other
species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to
define a set of masks in standard space (e.g. MNI152) define a set of masks in standard space (e.g. MNI152)
The script was written by Saad Jbabdi & Stamatios Sotiropoulos The script was written by Saad Jbabdi & Stamatios Sotiropoulos
...@@ -31,16 +31,16 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015 ...@@ -31,16 +31,16 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
--------------------------------------------------------------------- ---------------------------------------------------------------------
## Usage: ## Usage:
``` ```
__ _______ ____ _ ____ _____ __ _______ ____ _ ____ _____
\ \/ /_ _| _ \ / \ / ___|_ _| \ \/ /_ _| _ \ / \ / ___|_ _|
\ / | | | |_) | / _ \| | | | \ / | | | |_) | / _ \| | | |
/ \ | | | _ < / ___ \ |___ | | / \ | | | _ < / ___ \ |___ | |
/_/\_\ |_| |_| \_\/_/ \_\____| |_| /_/\_\ |_| |_| \_\/_/ \_\____| |_|
Usage:
Usage:
xtract -bpx <bedpostX_dir> -out <outputDir> -str <structuresFile> -p <protocolsFolder> [options] xtract -bpx <bedpostX_dir> -out <outputDir> -str <structuresFile> -p <protocolsFolder> [options]
xtract -bpx <bedpostX_dir> -out <outputDir> -species HUMAN [options] xtract -bpx <bedpostX_dir> -out <outputDir> -species HUMAN [options]
xtract -bpx <bedpostX_dir> -out <outputDir> -species MACAQUE [options] xtract -bpx <bedpostX_dir> -out <outputDir> -species MACAQUE [options]
...@@ -49,7 +49,7 @@ Usage: ...@@ -49,7 +49,7 @@ Usage:
-bpx <folder> Path to bedpostx folder -bpx <folder> Path to bedpostx folder
-out <folder> Path to output folder -out <folder> Path to output folder
And EITHER: And EITHER:
-str <file> Structures file (format: <tractName> [samples=1], 1 means 1000, '#' to skip lines) -str <file> Structures file (format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
-p <folder> Protocols folder (all masks in same standard space) -p <folder> Protocols folder (all masks in same standard space)
...@@ -59,8 +59,8 @@ Usage: ...@@ -59,8 +59,8 @@ Usage:
Optional arguments: Optional arguments:
-stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) -stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
-gpu Use GPU version -gpu Use GPU version
-native Run tractography in native (diffusion) space -native Run tractography in native (diffusion) space
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used) -res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
-ptx_options <options.txt> Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10) -ptx_options <options.txt> Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
...@@ -70,8 +70,8 @@ Usage: ...@@ -70,8 +70,8 @@ Usage:
--------------------------------------------------------------------- ---------------------------------------------------------------------
## Running XTRACT: ## Running XTRACT:
XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB. XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB.
For optimal performance, use the GPU version!!!! For optimal performance, use the GPU version!!!!
--------------------------------------------------------------------- ---------------------------------------------------------------------
...@@ -80,7 +80,7 @@ Usage: ...@@ -80,7 +80,7 @@ Usage:
- For HUMAN, XTRACT uses the MNI152 standard space in $FSLDIR/etc/standard - For HUMAN, XTRACT uses the MNI152 standard space in $FSLDIR/etc/standard
- For MACAQUE, XTRACT uses the F99 atlas in Caret - see http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases - For MACAQUE, XTRACT uses the F99 atlas in Caret - see http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases
We also provide a copy of the F99 atlas in $FSLDIR/etc/xtract_data/standard/F99. This includes a helper script for registering your own diffusion/structural data to the F99 altas We also provide a copy of the F99 atlas in $FSLDIR/etc/xtract_data/standard/F99. This includes a helper script for registering your own diffusion/structural data to the F99 altas
When running XTRACT with the '-species' option, a predefined list of tracts is automatically extracted. Currently the following tracts are available: When running XTRACT with the '-species' option, a predefined list of tracts is automatically extracted. Currently the following tracts are available:
...@@ -119,12 +119,12 @@ When running XTRACT with the '-species' option, a predefined list of tracts is a ...@@ -119,12 +119,12 @@ When running XTRACT with the '-species' option, a predefined list of tracts is a
Suppose you want to create an automated protocol for a tract called 'mytrack'. Suppose you want to create an automated protocol for a tract called 'mytrack'.
First you need to create a folder called 'mytrack' which you can add e.g. in the protocols folder. First you need to create a folder called 'mytrack' which you can add e.g. in the protocols folder.
Then create the following NIFTI files (with this exact naming) and copy them into mytrack: Then create the following NIFTI files (with this exact naming) and copy them into mytrack:
**Compulsory**: **Compulsory**:
- seed.nii.gz : a seed mask - seed.nii.gz : a seed mask
**Optional**: **Optional**:
- stop.nii.gz : a stop mask if required - stop.nii.gz : a stop mask if required
...@@ -133,7 +133,7 @@ Then create the following NIFTI files (with this exact naming) and copy them int ...@@ -133,7 +133,7 @@ Then create the following NIFTI files (with this exact naming) and copy them int
- target.nii.gz : a single target mask - target.nii.gz : a single target mask
- target1.nii.gz, target2.nii.gz, etc. : a number of targets, in which case streamlines will be kept if they cross ALL of them - target1.nii.gz, target2.nii.gz, etc. : a number of targets, in which case streamlines will be kept if they cross ALL of them
- invert (empty file to indicate that a seed->target and target->seed run will be added and combined) - invert (empty file to indicate that a seed->target and target->seed run will be added and combined)
if such an option is required a single "target.nii.gz" file is also expected if such an option is required a single "target.nii.gz" file is also expected
All the masks above should be in standard space (e.g. MNI152 or F99) if you want to run the same tracking for a collection of subjects. All the masks above should be in standard space (e.g. MNI152 or F99) if you want to run the same tracking for a collection of subjects.
...@@ -146,27 +146,33 @@ The output of XTRACT is a folder that contrains tracts in separate folders. We p ...@@ -146,27 +146,33 @@ The output of XTRACT is a folder that contrains tracts in separate folders. We p
``` ```
__ _______ ____ _ ____ _____ _ __ _______ ____ _ ____ _____ _
\ \/ /_ _| _ \ / \ / ___|_ _| __ _(_) _____ _____ _ __ \ \/ /_ _| _ \ / \ / ___|_ _| __ _(_) _____ _____ _ __
\ / | | | |_) | / _ \| | | | \ \ / / |/ _ \ \ /\ / / _ \ '__| \ / | | | |_) | / _ \| | | | \ \ / / |/ _ \ \ /\ / / _ \ '__|
/ \ | | | _ < / ___ \ |___ | | \ V /| | __/\ V V / __/ | / \ | | | _ < / ___ \ |___ | | \ V /| | __/\ V V / __/ |
/_/\_\ |_| |_| \_\/_/ \_\____| |_| \_/ |_|\___| \_/\_/ \___|_| /_/\_\ |_| |_| \_\/_/ \_\____| |_| \_/ |_|\___| \_/\_/ \___|_|
Usage:
xtract_viewer -dir <xtractDir> [options]
Compulsory arguments: Usage:
xtract_viewer -dir <xtractDir> -species HUMAN [options]
xtract_viewer -dir <xtractDir> -species MACAQUE [options]
xtract_viewer -dir <xtractDir> -brain <PATH> [options]
-dir FOLDER Path to XTRACT output folder Compulsory arguments:
Optional arguments: -dir <FOLDER> Path to XTRACT output folder
And EITHER:
-species <SPECIES> One of HUMAN or MACAQUE
OR:
-brain <PATH> The brain image to use for the background overlay - must be in the same space as tracts.
Default is the FSL_HCP065_FA map for HUMAN and F99 T1 brain for MACAQUE
-str STRUCTURE,STRUCTURE,... Structures (comma separated (default = display all that is found in input folder) Optional arguments:
-thr NUMBER NUMBER The lower and upper thresholds applied to the tracts for viewing -str STRUCTURE,STRUCTURE,... Structures (comma separated (default = display all that is found in input folder)
Default = 0.001 0.1
-brain The brain image to use for the background overlay - must be in the same space as tracts. -thr NUMBER NUMBER The lower and upper thresholds applied to the tracts for viewing
Default is the FSL_HCP065_FA map Default = 0.001 0.1
``` ```
...@@ -16,7 +16,7 @@ datadir=$FSLDIR/etc/xtract_data ...@@ -16,7 +16,7 @@ datadir=$FSLDIR/etc/xtract_data
Usage() { Usage() {
cat << EOF cat << EOF
Usage: Usage:
xtract -bpx <bedpostX_dir> -out <outputDir> -str <structuresFile> -p <protocolsFolder> [options] xtract -bpx <bedpostX_dir> -out <outputDir> -str <structuresFile> -p <protocolsFolder> [options]
xtract -bpx <bedpostX_dir> -out <outputDir> -species HUMAN [options] xtract -bpx <bedpostX_dir> -out <outputDir> -species HUMAN [options]
xtract -bpx <bedpostX_dir> -out <outputDir> -species MACAQUE [options] xtract -bpx <bedpostX_dir> -out <outputDir> -species MACAQUE [options]
...@@ -25,7 +25,7 @@ Usage: ...@@ -25,7 +25,7 @@ Usage:
-bpx <folder> Path to bedpostx folder -bpx <folder> Path to bedpostx folder
-out <folder> Path to output folder -out <folder> Path to output folder
And EITHER: And EITHER:
-str <file> Structures file (format: <tractName> [samples=1], 1 means 1000, '#' to skip lines) -str <file> Structures file (format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
-p <folder> Protocols folder (all masks in same standard space) -p <folder> Protocols folder (all masks in same standard space)
...@@ -35,8 +35,8 @@ Usage: ...@@ -35,8 +35,8 @@ Usage:
Optional arguments: Optional arguments:
-stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) -stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
-gpu Use GPU version -gpu Use GPU version
-native Run tractography in native (diffusion) space -native Run tractography in native (diffusion) space
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used) -res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
-ptx_options <options.txt> Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10) -ptx_options <options.txt> Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
...@@ -50,12 +50,12 @@ Splash (){ ...@@ -50,12 +50,12 @@ Splash (){
cat <<EOF cat <<EOF
__ _______ ____ _ ____ _____ __ _______ ____ _ ____ _____
\ \/ /_ _| _ \ / \ / ___|_ _| \ \/ /_ _| _ \ / \ / ___|_ _|
\ / | | | |_) | / _ \| | | | \ / | | | |_) | / _ \| | | |
/ \ | | | _ < / ___ \ |___ | | / \ | | | _ < / ___ \ |___ | |
/_/\_\ |_| |_| \_\/_/ \_\____| |_| /_/\_\ |_| |_| \_\/_/ \_\____| |_|
EOF EOF
} }
...@@ -64,7 +64,7 @@ Warning (){ ...@@ -64,7 +64,7 @@ Warning (){
cat <<EOF cat <<EOF
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
WARNING!!!! MACAQUE TRACTS ARE A WORK IN PROGRESS STILL.... WARNING!!!! MACAQUE TRACTS ARE A WORK IN PROGRESS STILL....
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
EOF EOF
} }
...@@ -219,13 +219,13 @@ while read structstring; do ...@@ -219,13 +219,13 @@ while read structstring; do
nseed=1 nseed=1
fi fi
nseed=$(echo "scale=0; 1000 * ${nseed} / 1"|bc) nseed=$(echo "scale=0; 1000 * ${nseed} / 1"|bc)
maskdir=$p/$struct maskdir=$p/$struct
# DEALING WITH RESAMPLING -- # DEALING WITH RESAMPLING --
# Pick space to run tractography in (diffusion or standard) # Pick space to run tractography in (diffusion or standard)
if [ "$nat" -eq 1 ];then if [ "$nat" -eq 1 ];then
echo " -- transforming masks into native space" echo " -- transforming masks into native space"
mkdir -p $out/masks/$struct mkdir -p $out/masks/$struct
for m in seed stop exclude;do for m in seed stop exclude;do
if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then
...@@ -233,22 +233,22 @@ while read structstring; do ...@@ -233,22 +233,22 @@ while read structstring; do
$FSLDIR/bin/fslmaths $out/masks/$struct/$m -thr 0.1 -bin $out/masks/$struct/$m -odt char $FSLDIR/bin/fslmaths $out/masks/$struct/$m -thr 0.1 -bin $out/masks/$struct/$m -odt char
fi fi
eval "${m}=$out/masks/$struct/$m" eval "${m}=$out/masks/$struct/$m"
done done
else else
for m in seed stop exclude;do for m in seed stop exclude;do
if [ $res -gt 0 ];then if [ $res -gt 0 ];then
# Resample at a different resolution # Resample at a different resolution
mkdir -p $out/masks/$struct mkdir -p $out/masks/$struct
if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then
$FSLDIR/bin/flirt -in $maskdir/$m -out $out/masks/$struct/$m -applyisoxfm $res -ref $maskdir/$m $FSLDIR/bin/flirt -in $maskdir/$m -out $out/masks/$struct/$m -applyisoxfm $res -ref $maskdir/$m
$FSLDIR/bin/fslmaths $out/masks/$struct/$m -thr 0.1 -bin $out/masks/$struct/$m -odt char $FSLDIR/bin/fslmaths $out/masks/$struct/$m -thr 0.1 -bin $out/masks/$struct/$m -odt char
fi fi
eval "${m}=$out/masks/$struct/$m" eval "${m}=$out/masks/$struct/$m"
else else
eval "${m}=$maskdir/$m" eval "${m}=$maskdir/$m"
fi fi
done done
fi fi
# Deal with targets (in cases where there may be more than one) # Deal with targets (in cases where there may be more than one)
targets=`imglob $maskdir/target*` targets=`imglob $maskdir/target*`
...@@ -276,7 +276,7 @@ while read structstring; do ...@@ -276,7 +276,7 @@ while read structstring; do
# Get generic options # Get generic options
o=$opts o=$opts
# Add inclusion/exclusion masks # Add inclusion/exclusion masks
if [ `$FSLDIR/bin/imtest $stop` -eq 1 ];then if [ `$FSLDIR/bin/imtest $stop` -eq 1 ];then
o="$o --stop=$stop" o="$o --stop=$stop"
...@@ -287,7 +287,7 @@ while read structstring; do ...@@ -287,7 +287,7 @@ while read structstring; do
# Add seed/target # Add seed/target
o1="$o --nsamples=$nseed -x $seed " o1="$o --nsamples=$nseed -x $seed "
if [ "x${targets}" != "x" ];then #Add waypoints if there are any if [ "x${targets}" != "x" ];then #Add waypoints if there are any
o1=" $o1 --waypoints=$targetfile " o1=" $o1 --waypoints=$targetfile "
fi fi
...@@ -295,8 +295,8 @@ while read structstring; do ...@@ -295,8 +295,8 @@ while read structstring; do
# Outputs # Outputs
o1=" $o1 -o density --dir=$out/tracts/$struct" o1=" $o1 -o density --dir=$out/tracts/$struct"
# Does the protocol define a second run with inverted seed / target masks? # Does the protocol define a second run with inverted seed / target masks?
if [ -e $maskdir/invert ]; then #Invert-mode if [ -e $maskdir/invert ]; then #Invert-mode
if [ `$FSLDIR/bin/imtest $maskdir/target.nii.gz` -eq 1 ];then # Check if a target.nii.gz image exists when invert option has been selected. if [ `$FSLDIR/bin/imtest $maskdir/target.nii.gz` -eq 1 ];then # Check if a target.nii.gz image exists when invert option has been selected.
mkdir -p $out/tracts/$struct/tractsInv mkdir -p $out/tracts/$struct/tractsInv
...@@ -311,8 +311,8 @@ while read structstring; do ...@@ -311,8 +311,8 @@ while read structstring; do
mergecmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/density -add $out/tracts/$struct/tractsInv/density $out/tracts/$struct/sum_density" mergecmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/density -add $out/tracts/$struct/tractsInv/density $out/tracts/$struct/sum_density"
#Add waypoints (create command but don't execute) #Add waypoints (create command but don't execute)
addcmd="echo \"scale=5; \`cat $out/tracts/$struct/waytotal\` + \`cat $out/tracts/$struct/tractsInv/waytotal\` \"|bc > $out/tracts/$struct/sum_waytotal" addcmd="echo \"scale=5; \`cat $out/tracts/$struct/waytotal\` + \`cat $out/tracts/$struct/tractsInv/waytotal\` \"|bc > $out/tracts/$struct/sum_waytotal"
# Waypoint normalisation (create command but don't execute) # Waypoint normalisation (create command but don't execute)
normcmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/sum_density -div \`cat $out/tracts/$struct/sum_waytotal\` $out/tracts/$struct/densityNorm" normcmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/sum_density -div \`cat $out/tracts/$struct/sum_waytotal\` $out/tracts/$struct/densityNorm"
...@@ -338,7 +338,7 @@ chmod +x $commands ...@@ -338,7 +338,7 @@ chmod +x $commands
if [ "x$SGE_ROOT" != "x" ]; then # Submit all commands to run in parallel on the cluster if [ "x$SGE_ROOT" != "x" ]; then # Submit all commands to run in parallel on the cluster
# One job per tract for a CPU cluster, one job for all tracts for a GPU cluster. # One job per tract for a CPU cluster, one job for all tracts for a GPU cluster.
if [ $gpu -eq 0 ];then if [ $gpu -eq 0 ];then
fsl_sub -q long.q -l $out/logs -N xtract -t $commands fsl_sub -q long.q -T 2160 -l $out/logs -N xtract -t $commands
else else
fsl_sub -q $FSLGECUDAQ -T 300 -l $out/logs -N xtract $commands fsl_sub -q $FSLGECUDAQ -T 300 -l $out/logs -N xtract $commands
fi fi
......
#!/bin/bash #!/bin/bash
# Copyright (C) 2019 University of Oxford # Copyright (C) 2019 University of Oxford
...@@ -14,11 +12,20 @@ Usage() { ...@@ -14,11 +12,20 @@ Usage() {
cat << EOF cat << EOF
Usage: Usage:
xtract_viewer -dir <xtractDir> [options] xtract_viewer -dir <xtractDir> -species HUMAN [options]
xtract_viewer -dir <xtractDir> -species MACAQUE [options]
xtract_viewer -dir <xtractDir> -brain <PATH> [options]
Compulsory arguments: Compulsory arguments:
-dir FOLDER Path to XTRACT output folder -dir <FOLDER> Path to XTRACT output folder
And EITHER:
-species <SPECIES> One of HUMAN or MACAQUE
OR:
-brain <PATH> The brain image to use for the background overlay - must be in the same space as tracts.
Default is the FSL_HCP065_FA map for HUMAN and F99 T1 brain for MACAQUE
Optional arguments: Optional arguments:
...@@ -27,8 +34,6 @@ Usage: ...@@ -27,8 +34,6 @@ Usage:
-thr NUMBER NUMBER The lower and upper thresholds applied to the tracts for viewing -thr NUMBER NUMBER The lower and upper thresholds applied to the tracts for viewing
Default = 0.001 0.1 Default = 0.001 0.1
-brain The brain image to use for the background overlay - must be in the same space as tracts.
Default is the FSL_HCP065_FA map
EOF EOF
exit 1 exit 1
} }
...@@ -37,12 +42,12 @@ Splash (){ ...@@ -37,12 +42,12 @@ Splash (){
cat <<EOF cat <<EOF
__ _______ ____ _ ____ _____ _ __ _______ ____ _ ____ _____ _
\ \/ /_ _| _ \ / \ / ___|_ _| __ _(_) _____ _____ _ __ \ \/ /_ _| _ \ / \ / ___|_ _| __ _(_) _____ _____ _ __
\ / | | | |_) | / _ \| | | | \ \ / / |/ _ \ \ /\ / / _ \ '__| \ / | | | |_) | / _ \| | | | \ \ / / |/ _ \ \ /\ / / _ \ '__|
/ \ | | | _ < / ___ \ |___ | | \ V /| | __/\ V V / __/ | / \ | | | _ < / ___ \ |___ | | \ V /| | __/\ V V / __/ |
/_/\_\ |_| |_| \_\/_/ \_\____| |_| \_/ |_|\___| \_/\_/ \___|_| /_/\_\ |_| |_| \_\/_/ \_\____| |_| \_/ |_|\___| \_/\_/ \___|_|
EOF EOF
} }
...@@ -59,11 +64,12 @@ cL="${#cmaps[@]}" # length of array for colourmap loop control ...@@ -59,11 +64,12 @@ cL="${#cmaps[@]}" # length of array for colourmap loop control
# Set defaults # Set defaults
thr=0.001 thr=0.001
uthr=0.1 uthr=0.1
brain=${FSLDIR}/data/standard/FSL_HCP1065_FA_1mm.nii.gz
str=ALL str=ALL
spec=""
while [ ! -z "$1" ];do while [ ! -z "$1" ];do
case "$1" in case "$1" in
-dir) dir=$2;shift;; -dir) dir=$2;shift;;
-species) spec=$2;shift;;
-str) IFS=', ' read -r -a str <<< "$2";shift;; -str) IFS=', ' read -r -a str <<< "$2";shift;;
-thr) thr=$2;uthr=$3;shift;shift;; -thr) thr=$2;uthr=$3;shift;shift;;
-brain) brain=$2;shift;; -brain) brain=$2;shift;;
...@@ -81,12 +87,26 @@ elif [ ! -d $dir ];then ...@@ -81,12 +87,26 @@ elif [ ! -d $dir ];then
echo "Xtract folder $dir not found" echo "Xtract folder $dir not found"
errflag=1 errflag=1
fi fi
if [ "$uthr" == "" ];then
echo "You have set a lower threshold but not an upper threshold. Must set '-thr' using <number> <number>" if [ "$spec" == "" ];then
if [ "$brain" == "" ];then
echo "Must set compulsory argument '-brain' OR specify '-species <SPECIES>'"
errflag=1
elif [ `$FSLDIR/bin/imtest $brain` -eq 0 ];then
echo "Brain overlay file $brain not found"
errflag=1
fi
elif [ $spec == HUMAN ];then
brain=${FSLDIR}/data/standard/FSL_HCP1065_FA_1mm.nii.gz
elif [ $spec == MACAQUE ];then
brain=${FSLDIR}/etc/xtract_data/standard/F99/mri/struct_brain.nii.gz
elif [ ! "$spec" == "HUMAN" ] && [ ! "$spec" == "MACAQUE" ];then
echo "Unrecognised option '$spec'. Must set '-species' using HUMAN or MACAQUE"
errflag=1 errflag=1
fi fi
if [ `$FSLDIR/bin/imtest $brain` -eq 0 ];then
echo "Brain overlay file $brain not found" if [ "$uthr" == "" ];then
echo "You have set a lower threshold but not an upper threshold. Must set '-thr' using <number> <number>"
errflag=1 errflag=1
fi fi
if [ "$errflag" -eq 1 ];then if [ "$errflag" -eq 1 ];then
...@@ -130,9 +150,9 @@ for tract in "${str[@]}";do ...@@ -130,9 +150,9 @@ for tract in "${str[@]}";do
else else
# if you find a left tract, then find the corresponding right tract # if you find a left tract, then find the corresponding right tract
# and colour in the same way # and colour in the same way
if [[ $tract == *"_l"* ]];then if [[ $tract == *"_l"* ]];then
tt=`echo ${tract} | sed s/_l/_r/` tt=`echo ${tract} | sed s/_l/_r/`
if [[ "${str[@]}" =~ "$tt" ]];then if [[ "${str[@]}" =~ "$tt" ]];then
# append _l and _r to fsleyes command with viewing options # append _l and _r to fsleyes command with viewing options
cmd="$cmd ${dir}/${preT}/${tract}${postT} $opts -cm ${cmaps[i]} -n ${tract} ${dir}/${preT}/${tt}${postT} $opts -cm ${cmaps[i]} -n ${tt}" cmd="$cmd ${dir}/${preT}/${tract}${postT} $opts -cm ${cmaps[i]} -n ${tract} ${dir}/${preT}/${tt}${postT} $opts -cm ${cmaps[i]} -n ${tt}"
else else
......
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