diff --git a/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh b/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh index db3707de0..1217be0e4 100755 --- a/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh +++ b/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh @@ -476,9 +476,8 @@ main() { done if [ ${Paired_flag} -eq 0 ]; then - log_Msg "Wrong Input! No pairs of phase encoding directions have been found!" - log_Msg "At least one pair is needed!" - exit 1 + log_Err "Wrong Input! No pairs of phase encoding directions have been found!" + log_Err_Abort "At least one pair is needed!" fi log_Msg "Running Intensity Normalisation" diff --git a/DiffusionPreprocessing/scripts/eddy_postproc.sh b/DiffusionPreprocessing/scripts/eddy_postproc.sh index de1fdec0e..a88cfaeb7 100755 --- a/DiffusionPreprocessing/scripts/eddy_postproc.sh +++ b/DiffusionPreprocessing/scripts/eddy_postproc.sh @@ -59,7 +59,7 @@ if [ ${CombineDataFlag} -eq 2 ]; then else echo "JAC resampling has been used. Eddy Output is now combined." PosVols=$(wc ${eddydir}/Pos.bval | awk {'print $2'}) - NegVols=$(wc ${eddydir}/Neg.bval | awk {'print $2'}) #Split Pos and Neg Volumes + NegVols=$(wc ${eddydir}/Neg.bval | awk {'print $2'}) # Split Pos and Neg Volumes ${FSLDIR}/bin/fslroi ${eddydir}/eddy_unwarped_images ${eddydir}/eddy_unwarped_Pos ${SelectBestB0} ${PosVols} # ignore extra first volume if ${SelectBestB0} is 1 ${FSLDIR}/bin/fslroi ${eddydir}/eddy_unwarped_images ${eddydir}/eddy_unwarped_Neg $((PosVols + ${SelectBestB0})) ${NegVols} # Note: 'eddy_combine' is apparently hard-coded to use "data" as the output NIFTI file name diff --git a/global/scripts/select_dwi_vols b/global/scripts/select_dwi_vols index 93e730e64..aa3d933fb 100755 --- a/global/scripts/select_dwi_vols +++ b/global/scripts/select_dwi_vols @@ -6,11 +6,12 @@ if [ "$4" == "" ];then echo "" echo " Optional arguments:" echo "" - echo " -b additional bvalues to be extracted (can be used multiple times)" - echo " -m output mean instead of concat" - echo " -v output variance instead of concat" - echo " -obv produce .bval and .bvec" - echo " -db only include volumes with offset in b-value less than this value (default: 100 s/mm2)" + echo " -b additional bvalues to be extracted (can be used multiple times)" + echo " -m output mean instead of concat" + echo " -v output variance instead of concat" + echo " -obv produce .bval and .bvec" + echo " -db only include volumes with offset in b-value less than" + echo " this value in either direction (default: 100 s/mm2)" echo "" exit 1 fi