tbss_3_postreg

#!/bin/sh

#   tbss_3_postreg - post-registration processing
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2005-2008 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
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#   
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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#   Oxford (the "Software")
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FSL_SUB=/usr/share/fsl/overlay/fsl_sub
export LC_ALL=C

Usage() {
    cat <<EOF

Usage: tbss_3_postreg [options]

Choose ONE of:
 -S   : derive mean_FA and mean_FA_skeleton from mean of all subjects in study (recommended)
 -T   : use FMRIB58_FA and its skeleton instead of study-derived mean and skeleton

EOF
    exit 1
}

[ "$1" = "" ] && Usage

if [ $1 = -S ] ; then
    SKELETON=0
elif [ $1 = -T ] ; then
    SKELETON=1
else
    Usage
fi

echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .tbsslog

cd FA

/bin/rm -f all.msf

if [ `${FSLDIR}/bin/imtest target` = 1 ] ; then
    echo "using pre-chosen target for registration"
    best=target
else
    echo "finding best target"

    n=`$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr* | wc -w`

    filelist=$($FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*)
    for f in $filelist ; do

	meanscore=0
	medianscore=0

	for g in $filelist; do

	    thismeanscore=`cat ${g}_to_${f}_warp.msf | awk '{print $1}'`
	    thismedianscore=`cat ${g}_to_${f}_warp.msf | awk '{print $2}'`

	    meanscore=`echo "10 k $meanscore $thismeanscore + p" | dc -`
	    medianscore=`echo "10 k $medianscore $thismedianscore + p" | dc -`
	done

	meanscore=`echo "10 k $meanscore $n / p" | dc -`
	medianscore=`echo "10 k $medianscore $n / p" | dc -`

	echo "$f $meanscore $medianscore"
	echo "$f $meanscore $medianscore" >> all.msf

    done

    best=`cat all.msf | sort -k 2 -n | head -n 1 | awk '{print $1}'`
    echo "best target is $best - now registering this to standard space"

    $FSLDIR/bin/imcp $best target
fi

echo $best > best.msf

mkdir -p ../stats

# is target already in MNI152 space? (kludge)
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

    echo "transforming all FA images into MNI152 space"
    filelist=`$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*`;
    # check that all the registration results are there!
    missingwarps="";
    for f in $filelist ; do
	if [ `${FSLDIR}/bin/imtest ${f}_to_target_warp` = 0 ] ; then
	    missingwarps="$missingwarps ${f}_to_target_warp"
	fi
    done
    if [ `echo $missingwarps | wc -c` -gt 1 ] ; then
	echo "ERROR:: cannot find the following warp results:"
	echo "    $missingwarps"
	echo "Please wait for registration (fnirt) to finish or re-run registrations";
	exit 1;
    fi
    for f in $filelist ; do
	    #echo $f
	    echo "$FSLDIR/bin/applywarp -i $f -o ${f}_to_target -r target -w ${f}_to_target_warp --rel" >> .commands.postreg
    done
    $FSL_SUB -m n -l tbss_logs -T 60 -N tbss_3_postreg -B -t .commands.postreg

else

    echo "affine-registering target to MNI152 space"
    $FSLDIR/bin/fslmaths target -bin target_mask
    $FSLDIR/bin/flirt -in target -inweight target_mask -ref $FSLDIR/data/standard/FMRIB58_FA_1mm -omat target_to_MNI152.mat -out target_to_MNI152

    echo "transforming (and upsampling) all FA images into MNI152 space"
    for f in `$FSLDIR/bin/imglob *_FA.nii* *_FA.img* *_FA.hdr*` ; do
	    #echo $f
	    echo "$FSLDIR/bin/applywarp -i $f -o ${f}_to_target -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w ${f}_to_${best}_warp --postmat=target_to_MNI152.mat" >> .commands.postreg
    done
    $FSL_SUB -m n  -l tbss_logs -T 60 -N tbss_3_postreg -B -t .commands.postreg

fi

# fsl_sub the following so we can request machines with loads of ram
# this is a workaround for fslmaths/fslmerge badly handling large datasets
memory="128g"
echo "merging all upsampled FA images into single 4D image"
echo "${FSLDIR}/bin/fslmerge -t ../stats/all_FA `$FSLDIR/bin/imglob *_FA_to_target.*`" > .commands
$FSL_SUB -m n  -l tbss_logs -T 1440 -N fslmerge -R $memory -B -t .commands

# create mean FA
echo "creating valid mask and mean FA"
cd ../stats
$FSL_SUB -m n  -l ../FA/tbss_logs -T 1440 -N mask_mean -R $memory -B  $FSLDIR/bin/fslmaths all_FA -max 0 -Tmin -bin mean_FA_mask -odt char
$FSL_SUB -m n  -l ../FA/tbss_logs -T 1440 -N mask_mean -R $memory -B  $FSLDIR/bin/fslmaths all_FA -mas mean_FA_mask all_FA
$FSL_SUB -m n  -l ../FA/tbss_logs -T 1440 -N mask_mean -R $memory -B  $FSLDIR/bin/fslmaths all_FA -Tmean mean_FA

# create skeleton
_SUB="$FSL_SUB -m n -l ../FA/tbss_logs -T 120 -N skeletonising -R $memory -B"
if [ $SKELETON = 0 ] ; then
    echo "skeletonising mean FA"
    $_SUB $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
else
    $_SUB $FSLDIR/bin/fslmaths $FSLDIR/data/standard/FMRIB58_FA_1mm -mas mean_FA_mask mean_FA
    $_SUB $FSLDIR/bin/fslmaths mean_FA -bin mean_FA_mask
    $_SUB $FSLDIR/bin/fslmaths all_FA -mas mean_FA_mask all_FA
    $_SUB $FSLDIR/bin/imcp $FSLDIR/data/standard/FMRIB58_FA-skeleton_1mm mean_FA_skeleton
fi

echo "now view mean_FA_skeleton to check whether the default threshold of 0.2 needs changing, when running:"
echo "tbss_4_prestats <threshold>"