From 2236c0f3c8f691b53bce2977fd6685e7b79c4e9d Mon Sep 17 00:00:00 2001
From: Taylor Hanayik <hanayik@gmail.com>
Date: Fri, 6 Oct 2023 15:27:28 +0100
Subject: [PATCH] move else statement to fix linear reg + bet
---
fsl_anat | 70 ++++++++++++++++++++++++++++++--------------------------
1 file changed, 37 insertions(+), 33 deletions(-)
diff --git a/fsl_anat b/fsl_anat
index 0d07ef8..2e3a21f 100755
--- a/fsl_anat
+++ b/fsl_anat
@@ -471,40 +471,44 @@ fi
#### REGISTRATION AND BRAIN EXTRACTION
# required input: ${T1}_biascorr
# output: ${T1}_biascorr_brain ${T1}_biascorr_brain_mask ${T1}_to_MNI_lin ${T1}_to_MNI [plus transforms, inverse transforms, jacobians, etc.]
-if [ $do_reg = yes ] ; then
- if [ $do_bet != yes ] ; then
- echo "Skipping registration, as it requires a non-brain-extracted input image"
- else
- date; echo "Registering to standard space (linear)"
- flirtargs="$flirtargs $nosearch"
- if [ $use_lesionmask = yes ] ; then flirtargs="$flirtargs -inweight lesionmaskinv" ; fi
- run $FSLDIR/bin/flirt -interp spline -dof 12 -in ${T1}_biascorr -ref $FSLDIR/data/standard/MNI152_${T1}_2mm -dof 12 -omat ${T1}_to_MNI_lin.mat -out ${T1}_to_MNI_lin $flirtargs
-
- if [ $do_nonlinreg = yes ] ; then
- date; echo "Registering to standard space (non-linear)"
- #refmask=$FSLDIR/data/standard/MNI152_${T1}_2mm_brain_mask_dil1
- refmask=MNI152_${T1}_2mm_brain_mask_dil1
- fnirtargs=""
- if [ $use_lesionmask = yes ] ; then fnirtargs="$fnirtargs --inmask=lesionmaskinv" ; fi
- run $FSLDIR/bin/fslmaths $FSLDIR/data/standard/MNI152_${T1}_2mm_brain_mask -fillh -dilF $refmask
- run $FSLDIR/bin/fnirt --in=${T1}_biascorr --ref=$FSLDIR/data/standard/MNI152_${T1}_2mm --fout=${T1}_to_MNI_nonlin_field --jout=${T1}_to_MNI_nonlin_jac --iout=${T1}_to_MNI_nonlin --logout=${T1}_to_MNI_nonlin.txt --cout=${T1}_to_MNI_nonlin_coeff --config=$FSLDIR/etc/flirtsch/${T1}_2_MNI152_2mm.cnf --aff=${T1}_to_MNI_lin.mat --refmask=$refmask $fnirtargs
-
- date; echo "Performing brain extraction (using FNIRT)"
- run $FSLDIR/bin/invwarp --ref=${T1}_biascorr -w ${T1}_to_MNI_nonlin_coeff -o MNI_to_${T1}_nonlin_field
- run $FSLDIR/bin/applywarp --interp=nn --in=$FSLDIR/data/standard/MNI152_${T1}_2mm_brain_mask --ref=${T1}_biascorr -w MNI_to_${T1}_nonlin_field -o ${T1}_biascorr_brain_mask
- run $FSLDIR/bin/fslmaths ${T1}_biascorr_brain_mask -fillh ${T1}_biascorr_brain_mask
- run $FSLDIR/bin/fslmaths ${T1}_biascorr -mas ${T1}_biascorr_brain_mask ${T1}_biascorr_brain
+if [ $do_reg = yes ]; then
+ if [ $do_bet != yes ]; then
+ echo "Skipping registration, as it requires a non-brain-extracted input image"
+ else
+ date
+ echo "Registering to standard space (linear)"
+ flirtargs="$flirtargs $nosearch"
+ if [ $use_lesionmask = yes ]; then flirtargs="$flirtargs -inweight lesionmaskinv"; fi
+ run $FSLDIR/bin/flirt -interp spline -dof 12 -in ${T1}_biascorr -ref $FSLDIR/data/standard/MNI152_${T1}_2mm -dof 12 -omat ${T1}_to_MNI_lin.mat -out ${T1}_to_MNI_lin $flirtargs
+
+ if [ $do_nonlinreg = yes ]; then
+ date
+ echo "Registering to standard space (non-linear)"
+ #refmask=$FSLDIR/data/standard/MNI152_${T1}_2mm_brain_mask_dil1
+ refmask=MNI152_${T1}_2mm_brain_mask_dil1
+ fnirtargs=""
+ if [ $use_lesionmask = yes ]; then fnirtargs="$fnirtargs --inmask=lesionmaskinv"; fi
+ run $FSLDIR/bin/fslmaths $FSLDIR/data/standard/MNI152_${T1}_2mm_brain_mask -fillh -dilF $refmask
+ run $FSLDIR/bin/fnirt --in=${T1}_biascorr --ref=$FSLDIR/data/standard/MNI152_${T1}_2mm --fout=${T1}_to_MNI_nonlin_field --jout=${T1}_to_MNI_nonlin_jac --iout=${T1}_to_MNI_nonlin --logout=${T1}_to_MNI_nonlin.txt --cout=${T1}_to_MNI_nonlin_coeff --config=$FSLDIR/etc/flirtsch/${T1}_2_MNI152_2mm.cnf --aff=${T1}_to_MNI_lin.mat --refmask=$refmask $fnirtargs
+
+ date
+ echo "Performing brain extraction (using FNIRT)"
+ run $FSLDIR/bin/invwarp --ref=${T1}_biascorr -w ${T1}_to_MNI_nonlin_coeff -o MNI_to_${T1}_nonlin_field
+ run $FSLDIR/bin/applywarp --interp=nn --in=$FSLDIR/data/standard/MNI152_${T1}_2mm_brain_mask --ref=${T1}_biascorr -w MNI_to_${T1}_nonlin_field -o ${T1}_biascorr_brain_mask
+ run $FSLDIR/bin/fslmaths ${T1}_biascorr_brain_mask -fillh ${T1}_biascorr_brain_mask
+ run $FSLDIR/bin/fslmaths ${T1}_biascorr -mas ${T1}_biascorr_brain_mask ${T1}_biascorr_brain
+ else
+ if [ $do_bet = yes ]; then
+ date
+ echo "Performing brain extraction (using BET)"
+ run $FSLDIR/bin/bet ${T1}_biascorr ${T1}_biascorr_brain -m $betopts ## results sensitive to the f parameter
+ else
+ run $FSLDIR/bin/fslmaths ${T1}_biascorr ${T1}_biascorr_brain
+ run $FSLDIR/bin/fslmaths ${T1}_biascorr_brain -bin ${T1}_biascorr_brain_mask
+ fi
+ fi
+ ## In the future, could check the initial ROI extraction here
fi
- ## In the future, could check the initial ROI extraction here
- fi
-else
- if [ $do_bet = yes ] ; then
- date; echo "Performing brain extraction (using BET)"
- run $FSLDIR/bin/bet ${T1}_biascorr ${T1}_biascorr_brain -m $betopts ## results sensitive to the f parameter
- else
- run $FSLDIR/bin/fslmaths ${T1}_biascorr ${T1}_biascorr_brain
- run $FSLDIR/bin/fslmaths ${T1}_biascorr_brain -bin ${T1}_biascorr_brain_mask
- fi
fi
--
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