diff --git a/bedpostx_preproc.sh b/bedpostx_preproc.sh index bb95ab4246bb031358d04c34e25dda9877f8023c..652c2503f4aa07d12baff8511248b73072a71b0b 100755 --- a/bedpostx_preproc.sh +++ b/bedpostx_preproc.sh @@ -1,6 +1,7 @@ #!/bin/sh subjdir=$1 +gflag=$2 echo Copying files to bedpost directory cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX @@ -12,4 +13,8 @@ fi ${FSLDIR}/bin/fslslice ${subjdir}/data ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask +if [ ${gflag} -eq 1 ]; then + ${FSLDIR}/bin/fslslice ${subjdir}/grad_dev +fi + echo Done