diff --git a/bedpostx_postproc.sh b/bedpostx_postproc.sh index c4afa024614e1ea95f31d289d5f440266fd33aae..55b3fdbdff9ae688195b03a450d6e032dcda10d7 100755 --- a/bedpostx_postproc.sh +++ b/bedpostx_postproc.sh @@ -30,11 +30,11 @@ do done if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then - ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsamples + ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsumsamples fib=1 while [ $fib -le $numfib ] do - fslmaths ${subjdir}.bedpostX/mean_fsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsamples + ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_fsumsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsumsamples fib=$(($fib + 1)) done fi @@ -63,13 +63,13 @@ fi echo Removing intermediate files -if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then - if [ `imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then - if [ `imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then +if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then + if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then + if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then rm -rf ${subjdir}.bedpostX/diff_slices rm -f ${subjdir}/data_slice_* rm -f ${subjdir}/nodif_brain_mask_slice_* - if [ `imtest ${subjdir}/grad_dev_slice_0000` -eq 1 ];then + if [ `${FSLDIR}/bin/imtest ${subjdir}/grad_dev_slice_0000` -eq 1 ];then rm -f ${subjdir}/grad_dev_slice_* fi fi