Removed obsolete bedpost scripts

bedpost_postproc.sh

-#!/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
\ No newline at end of file

bedpost_preproc.sh

-#!/bin/sh
-
-subjdir=$1
-
-#$ -S /bin/sh
-#$ -V
-#$ -N bp_preproc
-#$ -m a
-
-echo Copying files to bedpost directory
-cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpost
-${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpost
-${FSLDIR}/bin/avwmaths\
- ${subjdir}/nodif\
- -mas ${subjdir}/nodif_brain_mask\
- ${subjdir}.bedpost/nodif_brain
-
-${FSLDIR}/bin/avwslice ${subjdir}/data
-${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
-echo Done
\ No newline at end of file

bedpost_single_slice.sh

-#!/bin/sh
-
-subjdir=$1
-slice=`expr $SGE_TASK_ID - 1`
-slicezp=`${FSLDIR}/bin/zeropad $slice 4`
-
-#$ -cwd -q long.q
-#$ -S /bin/sh
-#$ -V -N bedpost
-#$ -m a
-
-${FSLDIR}/bin/diff_pvm\
- --data=$subjdir/data_slice_$slicezp\
- --mask=$subjdir/nodif_brain_mask_slice_$slicezp\
- -b $subjdir/bvals -r $subjdir/bvecs\
- --forcedir --logdir=$subjdir.bedpost/diff_slices/data_slice_$slicezp\
- --nj=1300 --bi=300 --se=20 > $subjdir.bedpost/logs/log$slicezp && echo Done