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#!/bin/sh
subjdir=$1
#$ -S /bin/sh
#$ -V
#$ -N bp_postproc
#$ -m ae
echo Merging outputs into 4D files
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpost/merged_thsamples ${subjdir}.bedpost/merged_phsamples ${subjdir}.bedpost/nodif_brain_mask ${subjdir}.bedpost/dyadic_vectors
echo Removing intermediate files
if [ `imtest ${subjdir}.bedpost/merged_thsamples` -eq 1 ];then
if [ `imtest ${subjdir}.bedpost/merged_phsamples` -eq 1 ];then
if [ `imtest ${subjdir}.bedpost/merged_fsamples` -eq 1 ];then
rm -rf ${subjdir}.bedpost/diff_slices
rm -f ${subjdir}/data_slice_*
rm -f ${subjdir}/nodif_brain_mask_slice_*
fi
fi
fi
echo Creating identity xfm
xfmdir=${subjdir}.bedpost/xfms
echo 1 0 0 0 > ${xfmdir}/eye.mat
echo 0 1 0 0 >> ${xfmdir}/eye.mat
echo 0 0 1 0 >> ${xfmdir}/eye.mat
echo 0 0 0 1 >> ${xfmdir}/eye.mat
echo Done