From c1f4ed8cdabd079ddda64ca90255ea12b0f68a19 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Tue, 23 Jun 2020 09:21:10 +0100
Subject: [PATCH] Addressed remaining of @harms commments

---
 DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh |  5 ++---
 DiffusionPreprocessing/scripts/eddy_postproc.sh       |  2 +-
 global/scripts/select_dwi_vols                        | 11 ++++++-----
 3 files changed, 9 insertions(+), 9 deletions(-)

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 <value>    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 <bvecs>  produce <output>.bval and <output>.bvec"
-    echo " -db <delta_bvals> only include volumes with offset in b-value less than this value (default: 100 s/mm2)"
+    echo " -b <value>        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 <bvecs>      produce <output>.bval and <output>.bvec"
+    echo " -db <delta_bvals> only include volumes with offset in b-value less than"
+    echo "                   this value in either direction (default: 100 s/mm2)"
     echo ""
     exit 1
 fi