diff --git a/bedpostx b/bedpostx index ebf7df1cb5a7ebacc09bc9ce26f2cb918648589e..9202f23acd50184ab0aa902977e03eb6145cbf42 100755 --- a/bedpostx +++ b/bedpostx @@ -17,7 +17,7 @@ Usage() { echo "Usage: bedpostx <subject directory> [options]" echo "" echo "expects to find bvals and bvecs in subject directory" - echo "expects to find data nodif_brain_mask nodif in subject directory" + echo "expects to find data and nodif_brain_mask in subject directory" echo "options:" echo "-n (number of fibres per voxel, default 2)" echo "-w (ARD weight, more weight means less fibres killed per voxel, default 1)" @@ -83,11 +83,6 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then exit 1 fi -if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` -eq 0 ]; then - echo "${subjdir}/nodif not found" - exit 1 -fi - if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then echo "${subjdir}/nodif_brain_mask not found" exit 1 diff --git a/bedpostx_preproc.sh b/bedpostx_preproc.sh index bdae3469c68f2c6083e739e8e6a7f48c66a3cfc0..90123ca5fca76cea110863770df045c50d08d7ed 100755 --- a/bedpostx_preproc.sh +++ b/bedpostx_preproc.sh @@ -11,7 +11,7 @@ subjdir=$1 echo Copying files to bedpost directory cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX -${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX +${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX ${FSLDIR}/bin/fslmaths\ ${subjdir}/nodif\ -mas ${subjdir}/nodif_brain_mask\