From 1956e7eaceef2c888732e8dbacea26e28a6daea2 Mon Sep 17 00:00:00 2001
From: Nick Tustison <ntustison@gmail.com>
Date: Thu, 2 May 2024 18:21:52 -0700
Subject: [PATCH] ENH: More than 10 modalities.

---
 Scripts/antsMultivariateTemplateConstruction.sh  | 4 ++--
 Scripts/antsMultivariateTemplateConstruction2.sh | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Scripts/antsMultivariateTemplateConstruction.sh b/Scripts/antsMultivariateTemplateConstruction.sh
index e99ea11a4..15c64e4ae 100755
--- a/Scripts/antsMultivariateTemplateConstruction.sh
+++ b/Scripts/antsMultivariateTemplateConstruction.sh
@@ -324,7 +324,7 @@ function shapeupdatetotemplate() {
     echo " shapeupdatetotemplate---voxel-wise averaging of the warped images to the current template"
     echo "--------------------------------------------------------------------------------------"
 
-    imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
+    imagelist=(`ls ${outputname}template-modality${whichtemplate}-*WarpedToTemplate.nii.gz`)
     if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]]
       then
         echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
@@ -1346,7 +1346,7 @@ while [[ $i -lt ${ITERATIONLIMIT} ]];
                 indir=`pwd`
             fi
             IMGbase=`basename ${IMAGESETARRAY[$l]}`
-            POO=${OUTPUTNAME}template${k}${IMGbase}
+            POO=${OUTPUTNAME}template-modality${k}-${IMGbase}
             OUTFN=${POO%.*.*}
             OUTFN=`basename ${OUTFN}`
             OUTFN="${OUTFN}${l}"
diff --git a/Scripts/antsMultivariateTemplateConstruction2.sh b/Scripts/antsMultivariateTemplateConstruction2.sh
index cab4c404c..bf0eeed35 100755
--- a/Scripts/antsMultivariateTemplateConstruction2.sh
+++ b/Scripts/antsMultivariateTemplateConstruction2.sh
@@ -387,7 +387,7 @@ function shapeupdatetotemplate() {
     #echo "    ImageSetStatistics $dim ${whichtemplate}WarpedToTemplateList.txt ${template} 0"
     echo "--------------------------------------------------------------------------------------"
 
-    imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
+    imagelist=(`ls ${outputname}template-modality${whichtemplate}-*WarpedToTemplate.nii.gz`)
     if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]]
       then
         echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
@@ -1469,7 +1469,7 @@ while [[ $i -lt ${ITERATIONLIMIT} ]];
                 indir=`pwd`
               fi
             IMGbase=`basename ${IMAGESETARRAY[$l]}`
-            OUTFN=${OUTPUTNAME}template${k}${IMGbase/%?(.nii.gz|.nii)}
+            OUTFN=${OUTPUTNAME}template-modality${k}-${IMGbase/%?(.nii.gz|.nii)}
             OUTFN=`basename ${OUTFN}`
             OUTFN="${OUTFN}${l}"
             DEFORMED="${outdir}/${OUTFN}${l}WarpedToTemplate.nii.gz"