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Commit 3cbf6413 authored by Taylor Hanayik's avatar Taylor Hanayik
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convert indentations to spaces

parent 2236c0f3
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1 merge request!3fix fsl_anat nonlinreg failure
Pipeline #20605 skipped
Stage: fsl-ci-build
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......@@ -55,15 +55,15 @@ get_opt1() {
# get arg for -- options
get_arg1() {
if [ X`echo $1 | grep '='` = X ] ; then
echo "Option $1 requires an argument" 1>&2
exit 1
echo "Option $1 requires an argument" 1>&2
exit 1
else
arg=`echo $1 | sed 's/.*=//'`
if [ X$arg = X ] ; then
echo "Option $1 requires an argument" 1>&2
exit 1
fi
echo $arg
arg=`echo $1 | sed 's/.*=//'`
if [ X$arg = X ] ; then
echo "Option $1 requires an argument" 1>&2
exit 1
fi
echo $arg
fi
}
......@@ -77,8 +77,8 @@ get_imarg1() {
# get arg for - options (need to pass both $1 and $2 to this)
get_arg2() {
if [ X$2 = X ] ; then
echo "Option $1 requires an argument" 1>&2
exit 1
echo "Option $1 requires an argument" 1>&2
exit 1
fi
echo $2
}
......@@ -143,91 +143,91 @@ if [ $# -lt 2 ] ; then Usage; exit 1; fi
while [ $# -ge 1 ] ; do
iarg=`get_opt1 $1`;
case "$iarg"
in
-i)
inputimage=`get_imarg2 $1 $2`;
shift 2;;
-o)
outputname=`get_arg2 $1 $2`;
shift 2;;
-d)
anatdir=`get_arg2 $1 $2`;
shift 2;;
-s)
smooth=`get_arg2 $1 $2`;
shift 2;;
-m)
use_lesionmask=yes;
lesionmask=`get_arg2 $1 $2`;
shift 2;;
-t)
typestr=`get_arg2 $1 $2`;
if [ $typestr = T1 ] ; then type=1; fi
if [ $typestr = T2 ] ; then type=2; fi
if [ $typestr = PD ] ; then type=3; fi
shift 2;;
--list)
imagelist=`get_arg1 $1`;
multipleimages=yes;
shift;;
--clobber)
clobber=yes;
shift;;
--noreorient)
do_reorient=no;
shift;;
--nocrop)
do_crop=no;
shift;;
--nobet)
do_bet=no;
shift;;
--noreg)
do_reg=no;
shift;;
--nononlinreg)
do_nonlinreg=no;
shift;;
--noseg)
do_seg=no;
shift;;
--nosubcortseg)
do_subcortseg=no;
shift;;
--nobias)
do_biasrestore=no;
shift;;
--nosearch)
nosearch=-nosearch;
shift;;
--strongbias)
strongbias=yes;
niter=5;
smooth=10;
shift;;
--weakbias)
strongbias=no;
niter=10;
smooth=20;
shift;;
--betfparam)
betfparam=`get_arg1 $1`;
shift;;
--nocleanup)
do_cleanup=no;
shift;;
-v)
verbose=yes;
shift;;
-h)
Usage;
exit 0;;
*)
#if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then
echo "Unrecognised option $1" 1>&2
exit 1
#fi
#shift;;
in
-i)
inputimage=`get_imarg2 $1 $2`;
shift 2;;
-o)
outputname=`get_arg2 $1 $2`;
shift 2;;
-d)
anatdir=`get_arg2 $1 $2`;
shift 2;;
-s)
smooth=`get_arg2 $1 $2`;
shift 2;;
-m)
use_lesionmask=yes;
lesionmask=`get_arg2 $1 $2`;
shift 2;;
-t)
typestr=`get_arg2 $1 $2`;
if [ $typestr = T1 ] ; then type=1; fi
if [ $typestr = T2 ] ; then type=2; fi
if [ $typestr = PD ] ; then type=3; fi
shift 2;;
--list)
imagelist=`get_arg1 $1`;
multipleimages=yes;
shift;;
--clobber)
clobber=yes;
shift;;
--noreorient)
do_reorient=no;
shift;;
--nocrop)
do_crop=no;
shift;;
--nobet)
do_bet=no;
shift;;
--noreg)
do_reg=no;
shift;;
--nononlinreg)
do_nonlinreg=no;
shift;;
--noseg)
do_seg=no;
shift;;
--nosubcortseg)
do_subcortseg=no;
shift;;
--nobias)
do_biasrestore=no;
shift;;
--nosearch)
nosearch=-nosearch;
shift;;
--strongbias)
strongbias=yes;
niter=5;
smooth=10;
shift;;
--weakbias)
strongbias=no;
niter=10;
smooth=20;
shift;;
--betfparam)
betfparam=`get_arg1 $1`;
shift;;
--nocleanup)
do_cleanup=no;
shift;;
-v)
verbose=yes;
shift;;
-h)
Usage;
exit 0;;
*)
#if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then
echo "Unrecognised option $1" 1>&2
exit 1
#fi
#shift;;
esac
done
......@@ -241,12 +241,12 @@ fi
if [ $type != 1 ] ; then
if [ $do_nonlinreg = yes ] ; then
echo "ERROR: Cannot do non-linear registration with non-T1 images, please re-run with --nononlinreg" ;
exit 1;
echo "ERROR: Cannot do non-linear registration with non-T1 images, please re-run with --nononlinreg" ;
exit 1;
fi ;
if [ $do_subcortseg = yes ] ; then
echo "ERROR: Cannot perform subcortical segmentation (with FIRST) on a non-T1 image, please re-run with --nosubcortseg"
exit 1;
echo "ERROR: Cannot perform subcortical segmentation (with FIRST) on a non-T1 image, please re-run with --nosubcortseg"
exit 1;
fi ;
fi
......@@ -262,32 +262,32 @@ betopts="-f ${betfparam}"
if [ X$anatdir = X ] ; then
if [ X${outputname} = X ] ; then
outputname=$inputimage;
outputname=$inputimage;
fi
if [ -d ${outputname}.anat ] ; then
if [ $clobber = no ] ; then
echo "ERROR: Directory ${outputname}.anat already exists!"
exit 1;
else
rm -rf ${outputname}.anat
fi
if [ $clobber = no ] ; then
echo "ERROR: Directory ${outputname}.anat already exists!"
exit 1;
else
rm -rf ${outputname}.anat
fi
fi
mkdir ${outputname}.anat
else
if [ X${inputimage} != X ] ; then
echo "ERROR: Cannot specify both -d and -i";
exit 1;
echo "ERROR: Cannot specify both -d and -i";
exit 1;
fi
if [ $multipleimages = yes ] ; then
echo "ERROR: Cannot specify both -d and --list";
exit 1;
echo "ERROR: Cannot specify both -d and --list";
exit 1;
fi
outputname=`$FSLDIR/bin/fsl_abspath $anatdir`;
outputname=`echo $outputname | sed 's/\.anat$//'`;
if [ ! -d ${outputname}.anat ] ; then
echo "ERROR: Directory ${outputname}.anat not found"
exit 1;
echo "ERROR: Directory ${outputname}.anat not found"
exit 1;
fi
inputimage=$anatdir/T1
fi
......@@ -298,23 +298,23 @@ echo "Output directory = ${outputname}.anat" >> ${outputname}.anat/$LOGFILE
if [ $multipleimages = yes ] ; then
if [ X${inputimage} != X ] ; then
echo "ERROR: Cannot specify both -i and --list";
exit 1;
echo "ERROR: Cannot specify both -i and --list";
exit 1;
fi
im1=`echo $imagelist | sed 's/,/ /g' | awk '{ print $1 }'`;
if [ $FSLDIR/bin/imtest $im1 = 1 ] ; then
# this is a comma separated list of image names
namelist="`echo ${imagelist} | sed 's/,/ /g'`";
# this is a comma separated list of image names
namelist="`echo ${imagelist} | sed 's/,/ /g'`";
else
# this is a file containing the image names
namelist="`cat ${imagelist}`";
# this is a file containing the image names
namelist="`cat ${imagelist}`";
fi
for name in $namelist ; do
if [ $FSLDIR/bin/imtest $name = 0 ] ; then
echo "ERROR: Cannot find image $name"
exit 1;
fi
$FSLDIR/bin/fslmaths $name ${outputname}.anat/${T1}_${num}
if [ $FSLDIR/bin/imtest $name = 0 ] ; then
echo "ERROR: Cannot find image $name"
exit 1;
fi
$FSLDIR/bin/fslmaths $name ${outputname}.anat/${T1}_${num}
done
echo "Input images are ${namelist}" >> ${outputname}.anat/$LOGFILE
else
......@@ -351,12 +351,12 @@ minval=`$FSLDIR/bin/fslstats ${T1} -p 0`;
maxval=`$FSLDIR/bin/fslstats ${T1} -p 100`;
if [ X`echo "if ( $minval < 0 ) { 1 }" | bc -l` = X1 ] ; then
if [ X`echo "if ( $maxval > 0 ) { 1 }" | bc -l` = X1 ] ; then
# if there are just some negative values among the positive ones then reset zero to the min value
run ${FSLDIR}/bin/fslmaths ${T1} -sub $minval ${T1} -odt float
# if there are just some negative values among the positive ones then reset zero to the min value
run ${FSLDIR}/bin/fslmaths ${T1} -sub $minval ${T1} -odt float
else
# if all values are negative then make them positive, but retain any zeros as zeros
run ${FSLDIR}/bin/fslmaths ${T1} -bin -binv zeromask
run ${FSLDIR}/bin/fslmaths ${T1} -sub $minval -mas zeromask ${T1} -odt float
# if all values are negative then make them positive, but retain any zeros as zeros
run ${FSLDIR}/bin/fslmaths ${T1} -bin -binv zeromask
run ${FSLDIR}/bin/fslmaths ${T1} -sub $minval -mas zeromask ${T1} -odt float
fi
fi
......@@ -382,9 +382,9 @@ if [ $do_crop = yes ] ; then
run $FSLDIR/bin/robustfov -i ${T1}_fullfov -r ${T1} -m ${T1}_roi2nonroi.mat | grep [0-9] | tail -1 > ${T1}_roi.log
# combine this mat file and the one above (if generated)
if [ $do_reorient = yes ] ; then
run $FSLDIR/bin/convert_xfm -omat ${T1}_nonroi2roi.mat -inverse ${T1}_roi2nonroi.mat
run $FSLDIR/bin/convert_xfm -omat ${T1}_orig2roi.mat -concat ${T1}_nonroi2roi.mat ${T1}_orig2std.mat
run $FSLDIR/bin/convert_xfm -omat ${T1}_roi2orig.mat -inverse ${T1}_orig2roi.mat
run $FSLDIR/bin/convert_xfm -omat ${T1}_nonroi2roi.mat -inverse ${T1}_roi2nonroi.mat
run $FSLDIR/bin/convert_xfm -omat ${T1}_orig2roi.mat -concat ${T1}_nonroi2roi.mat ${T1}_orig2std.mat
run $FSLDIR/bin/convert_xfm -omat ${T1}_roi2orig.mat -inverse ${T1}_orig2roi.mat
fi
fi
......@@ -395,8 +395,8 @@ if [ $use_lesionmask = yes ] ; then
if [ -f ${T1}_orig2std.mat ] ; then transform=${T1}_orig2std.mat ; fi
if [ -f ${T1}_orig2roi.mat ] ; then transform=${T1}_orig2roi.mat ; fi # this takes precedence if both exist
if [ X$transform != X ] ; then
$FSLDIR/bin/fslmaths lesionmask lesionmask_orig
$FSLDIR/bin/flirt -in lesionmask_orig -ref ${T1} -applyxfm -interp nearestneighbour -init ${transform} -out lesionmask
$FSLDIR/bin/fslmaths lesionmask lesionmask_orig
$FSLDIR/bin/flirt -in lesionmask_orig -ref ${T1} -applyxfm -interp nearestneighbour -init ${transform} -out lesionmask
fi
else
$FSLDIR/bin/fslmaths ${T1} -mul 0 lesionmask
......@@ -410,44 +410,44 @@ $FSLDIR/bin/fslmaths lesionmask -binv lesionmaskinv
# output: ${T1}_biascorr [ other intermediates to be cleaned up ]
if [ $do_biasrestore = yes ] ; then
if [ $strongbias = yes ] ; then
date; echo "Estimating and removing field (stage 1 - large-scale fields)"
# for the first step (very gross bias field) don't worry about the lesionmask
# the following is a replacement for : run $FSLDIR/bin/fslmaths ${T1} -s 20 ${T1}_s20
quick_smooth ${T1} ${T1}_s20
run $FSLDIR/bin/fslmaths ${T1} -div ${T1}_s20 ${T1}_hpf
if [ $do_bet = yes ] ; then
date; echo "Estimating and removing field (stage 1 - large-scale fields)"
# for the first step (very gross bias field) don't worry about the lesionmask
# the following is a replacement for : run $FSLDIR/bin/fslmaths ${T1} -s 20 ${T1}_s20
quick_smooth ${T1} ${T1}_s20
run $FSLDIR/bin/fslmaths ${T1} -div ${T1}_s20 ${T1}_hpf
if [ $do_bet = yes ] ; then
# get a rough brain mask - it can be *VERY* rough (i.e. missing huge portions of the brain or including non-brain, but non-background) - use -f 0.1 to err on being over inclusive
run $FSLDIR/bin/bet ${T1}_hpf ${T1}_hpf_brain -m -f 0.1
else
run $FSLDIR/bin/fslmaths ${T1}_hpf ${T1}_hpf_brain
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain -bin ${T1}_hpf_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask -mas lesionmaskinv ${T1}_hpf_brain_mask
run $FSLDIR/bin/bet ${T1}_hpf ${T1}_hpf_brain -m -f 0.1
else
run $FSLDIR/bin/fslmaths ${T1}_hpf ${T1}_hpf_brain
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain -bin ${T1}_hpf_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask -mas lesionmaskinv ${T1}_hpf_brain_mask
# get a smoothed version without the edge effects
run $FSLDIR/bin/fslmaths ${T1} -mas ${T1}_hpf_brain_mask ${T1}_hpf_s20
quick_smooth ${T1}_hpf_s20 ${T1}_hpf_s20
quick_smooth ${T1}_hpf_brain_mask ${T1}_initmask_s20
run $FSLDIR/bin/fslmaths ${T1}_hpf_s20 -div ${T1}_initmask_s20 -mas ${T1}_hpf_brain_mask ${T1}_hpf2_s20
run $FSLDIR/bin/fslmaths ${T1} -mas ${T1}_hpf_brain_mask -div ${T1}_hpf2_s20 ${T1}_hpf2_brain
# make sure the overall scaling doesn't change (equate medians)
med0=`$FSLDIR/bin/fslstats ${T1} -k ${T1}_hpf_brain_mask -P 50`;
med1=`$FSLDIR/bin/fslstats ${T1}_hpf2_brain -k ${T1}_hpf_brain_mask -P 50`;
run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -div $med1 -mul $med0 ${T1}_hpf2_brain
date; echo "Estimating and removing bias field (stage 2 - detailed fields)"
run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -mas lesionmaskinv ${T1}_hpf2_maskedbrain
run $FSLDIR/bin/fast -o ${T1}_initfast -l ${smooth} -b -B -t $type --iter=${niter} --nopve --fixed=0 -v ${T1}_hpf2_maskedbrain
run $FSLDIR/bin/fslmaths ${T1}_initfast_restore -mas lesionmaskinv ${T1}_initfast_maskedrestore
run $FSLDIR/bin/fast -o ${T1}_initfast2 -l ${smooth} -b -B -t $type --iter=${niter} --nopve --fixed=0 -v ${T1}_initfast_maskedrestore
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask ${T1}_initfast2_brain_mask
run $FSLDIR/bin/fslmaths ${T1} -mas ${T1}_hpf_brain_mask ${T1}_hpf_s20
quick_smooth ${T1}_hpf_s20 ${T1}_hpf_s20
quick_smooth ${T1}_hpf_brain_mask ${T1}_initmask_s20
run $FSLDIR/bin/fslmaths ${T1}_hpf_s20 -div ${T1}_initmask_s20 -mas ${T1}_hpf_brain_mask ${T1}_hpf2_s20
run $FSLDIR/bin/fslmaths ${T1} -mas ${T1}_hpf_brain_mask -div ${T1}_hpf2_s20 ${T1}_hpf2_brain
# make sure the overall scaling doesn't change (equate medians)
med0=`$FSLDIR/bin/fslstats ${T1} -k ${T1}_hpf_brain_mask -P 50`;
med1=`$FSLDIR/bin/fslstats ${T1}_hpf2_brain -k ${T1}_hpf_brain_mask -P 50`;
run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -div $med1 -mul $med0 ${T1}_hpf2_brain
date; echo "Estimating and removing bias field (stage 2 - detailed fields)"
run $FSLDIR/bin/fslmaths ${T1}_hpf2_brain -mas lesionmaskinv ${T1}_hpf2_maskedbrain
run $FSLDIR/bin/fast -o ${T1}_initfast -l ${smooth} -b -B -t $type --iter=${niter} --nopve --fixed=0 -v ${T1}_hpf2_maskedbrain
run $FSLDIR/bin/fslmaths ${T1}_initfast_restore -mas lesionmaskinv ${T1}_initfast_maskedrestore
run $FSLDIR/bin/fast -o ${T1}_initfast2 -l ${smooth} -b -B -t $type --iter=${niter} --nopve --fixed=0 -v ${T1}_initfast_maskedrestore
run $FSLDIR/bin/fslmaths ${T1}_hpf_brain_mask ${T1}_initfast2_brain_mask
else
if [ $do_bet = yes ] ; then
if [ $do_bet = yes ] ; then
# get a rough brain mask - it can be *VERY* rough (i.e. missing huge portions of the brain or including non-brain, but non-background) - use -f 0.1 to err on being over inclusive
run $FSLDIR/bin/bet ${T1} ${T1}_initfast2_brain -m -f 0.1
else
run $FSLDIR/bin/fslmaths ${T1} ${T1}_initfast2_brain
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain -bin ${T1}_initfast2_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain ${T1}_initfast2_restore
run $FSLDIR/bin/bet ${T1} ${T1}_initfast2_brain -m -f 0.1
else
run $FSLDIR/bin/fslmaths ${T1} ${T1}_initfast2_brain
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain -bin ${T1}_initfast2_brain_mask
fi
run $FSLDIR/bin/fslmaths ${T1}_initfast2_brain ${T1}_initfast2_restore
fi
# redo fast again to try and improve bias field
run $FSLDIR/bin/fslmaths ${T1}_initfast2_restore -mas lesionmaskinv ${T1}_initfast2_maskedrestore
......@@ -472,43 +472,43 @@ fi
# 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
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
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
fi
......@@ -532,7 +532,7 @@ if [ $do_seg = yes ] ; then
run $FSLDIR/bin/fslmaths ${T1}_biascorr_init -div ${T1}_fast_bias ${T1}_biascorr
if [ $do_nonlinreg = yes ] ; then
# regenerate the standard space version with the new bias field correction applied
run $FSLDIR/bin/applywarp -i ${T1}_biascorr -w ${T1}_to_MNI_nonlin_field -r $FSLDIR/data/standard/MNI152_${T1}_2mm -o ${T1}_to_MNI_nonlin --interp=spline
run $FSLDIR/bin/applywarp -i ${T1}_biascorr -w ${T1}_to_MNI_nonlin_field -r $FSLDIR/data/standard/MNI152_${T1}_2mm -o ${T1}_to_MNI_nonlin --interp=spline
fi
fi
......@@ -545,7 +545,7 @@ if [ $do_reg = yes ] && [ $do_seg = yes ] && [ $T1 = T1 ] ; then
run ${FSLDIR}/bin/bet ${T1}_biascorr ${T1}_biascorr_bet -s -m $betopts
run ${FSLDIR}/bin/pairreg ${FSLDIR}/data/standard/MNI152_T1_2mm_brain ${T1}_biascorr_bet ${FSLDIR}/data/standard/MNI152_T1_2mm_skull ${T1}_biascorr_bet_skull ${T1}2std_skullcon.mat
if [ $use_lesionmask = yes ] ; then
run ${FSLDIR}/bin/fslmaths lesionmask -max ${T1}_fast_pve_2 ${T1}_fast_pve_2_plusmask -odt float
run ${FSLDIR}/bin/fslmaths lesionmask -max ${T1}_fast_pve_2 ${T1}_fast_pve_2_plusmask -odt float
# ${FSLDIR}/bin/fslmaths lesionmask -bin -mul 3 -max ${T1}_fast_seg ${T1}_fast_seg_plusmask -odt int
fi
vscale=`${FSLDIR}/bin/avscale ${T1}2std_skullcon.mat | grep Determinant | awk '{ print $3 }'`;
......
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