From 58e32102e5bbee10e92bdd87240c01e866fa017e Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Sat, 26 Aug 2023 16:36:48 -0400
Subject: [PATCH] Fix: don't repeat N4 every iteration

---
 Scripts/antsMultivariateTemplateConstruction.sh  | 6 ++++--
 Scripts/antsMultivariateTemplateConstruction2.sh | 7 ++++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/Scripts/antsMultivariateTemplateConstruction.sh b/Scripts/antsMultivariateTemplateConstruction.sh
index cf5827e6e..8eb11b775 100755
--- a/Scripts/antsMultivariateTemplateConstruction.sh
+++ b/Scripts/antsMultivariateTemplateConstruction.sh
@@ -1360,8 +1360,10 @@ while [[ $i -lt ${ITERATIONLIMIT} ]];
             if [[ $N4CORRECT -eq 1 ]];
               then
                 REPAIRED="${outdir}/${OUTFN}Repaired.nii.gz"
-                exe=" $exe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2\n"
-                pexe=" $pexe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2  >> ${outdir}/job_${count}_metriclog.txt\n"
+                if [[ ! -s ${REPAIRED} ]]; then
+                  exe=" $exe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2\n"
+                  pexe=" $pexe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2  >> ${outdir}/job_${count}_metriclog.txt\n"
+                fi
                 IMAGEMETRICSET="$IMAGEMETRICSET -m ${METRIC}${TEMPLATES[$k]},${REPAIRED},${METRICPARAMS}"
                 warpexe=" $warpexe ${WARP} ${DIM} ${REPAIRED} ${DEFORMED} -R ${TEMPLATES[$k]} ${outdir}/${OUTWARPFN}Warp.nii.gz ${outdir}/${OUTWARPFN}Affine.txt\n"
                 warppexe=" $warppexe ${WARP} ${DIM} ${REPAIRED} ${DEFORMED} -R ${TEMPLATES[$k]} ${outdir}/${OUTWARPFN}Warp.nii.gz ${outdir}/${OUTWARPFN}Affine.txt >> ${outdir}/job_${count}_metriclog.txt\n"
diff --git a/Scripts/antsMultivariateTemplateConstruction2.sh b/Scripts/antsMultivariateTemplateConstruction2.sh
index 583d8a8e0..01f81d333 100755
--- a/Scripts/antsMultivariateTemplateConstruction2.sh
+++ b/Scripts/antsMultivariateTemplateConstruction2.sh
@@ -1488,9 +1488,10 @@ while [[ $i -lt ${ITERATIONLIMIT} ]];
             if [[ $N4CORRECT -eq 1 ]];
               then
                 REPAIRED="${outdir}/${OUTFN}Repaired.nii.gz"
-                exe=" $exe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2 --verbose 1\n"
-                pexe=" $pexe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2 --verbose 1  >> ${outdir}/job_${count}_metriclog.txt >> ${outdir}/job_${count}_metriclog.txt\n"
-
+                if [[ ! -s ${REPAIRED} ]]; then
+                  exe=" $exe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2 --verbose 1\n"
+                  pexe=" $pexe $N4 -d ${DIM} -b [ 200 ] -c [ 50x50x40x30,0.00000001 ] -i ${IMAGESETARRAY[$l]} -o ${REPAIRED} -r 0 -s 2 --verbose 1  >> ${outdir}/job_${count}_metriclog.txt >> ${outdir}/job_${count}_metriclog.txt\n"
+                fi
                 IMAGEMETRICSET="$IMAGEMETRICSET -m ${METRIC}${TEMPLATES[$k]},${REPAIRED},${METRICPARAMS}"
                 IMAGEMETRICLINEARSET="$IMAGEMETRICLINEARSET -m MI[ ${TEMPLATES[$k]},${REPAIRED},${MODALITYWEIGHTS[$k]},32,Regular,0.25 ]"