diff --git a/rubix_preproc.sh b/rubix_preproc.sh index f797f7a878c9c53e7b8e0c6f34723ecd05db711c..222983c1309f25606bcff458d93e3aba1467f55d 100644 --- a/rubix_preproc.sh +++ b/rubix_preproc.sh @@ -13,7 +13,7 @@ if [ ${filterflag} -eq 1 ]; then cp ${subjdir}/bvecs $out_dir/bvecsHR cp ${subjdir}/bvals $out_dir/bvalsHR ${FSLDIR}/bin/fslslice $subjdir/data $out_dir/dataHR - HighRes=`fslval ${subjdir}/data pixdim1` + HighRes=`${FSLDIR}/bin/fslval ${subjdir}/data pixdim1` LowRes=`echo "${HighRes} * 2" | bc -l` echo "Create Downsampled version of data at ${LowRes} mm isotropic" ${FSLDIR}/bin/flirt -in ${subjdir}/nodif_brain_mask -ref ${subjdir}/nodif_brain_mask -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/nodif_brain_maskLR