diff --git a/fsl_anat b/fsl_anat
index 2e3a21f8e9edd2636152f798c05393d9d8ef67f0..b8dc4c069694eeb9fe7f6d7491443c2560ab2b02 100755
--- a/fsl_anat
+++ b/fsl_anat
@@ -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 }'`;