remove nodif

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

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\