From d01b387ba4f73470d09e7829151bf27dd2abccd0 Mon Sep 17 00:00:00 2001
From: thomshaw92 <thomasbasilshaw@gmail.com>
Date: Wed, 15 Jul 2020 13:26:56 +1000
Subject: [PATCH] Final bugs squashed. Tested and working

---
 LASHiS.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/LASHiS.sh b/LASHiS.sh
index 5a34de8..43b94ad 100755
--- a/LASHiS.sh
+++ b/LASHiS.sh
@@ -639,15 +639,14 @@ fi
 
 #apply the warp from the template to the original images (both T1w and T2w) - with themselves as the reference
 SUBJECT_COUNT=0
+WARP_COUNT=0
 for (( i=0; i < ${#ANATOMICAL_IMAGES[@]}; i+=$NUMBER_OF_MODALITIES ))
 do
     BASENAME_ID=`basename ${ANATOMICAL_IMAGES[$i]}`
     BASENAME_ID=${BASENAME_ID/\.nii\.gz/}
     BASENAME_ID=${BASENAME_ID/\.nii/}
-    
     OUTPUT_DIRECTORY_FOR_SINGLE_SUBJECT_ASHS=${OUTPUT_DIR}/${BASENAME_ID}
     OUTPUT_DIRECTORY_FOR_SINGLE_SUBJECT_ASHS=${OUTPUT_DIRECTORY_FOR_SINGLE_SUBJECT_ASHS}_${SUBJECT_COUNT}
-    WARP_COUNT=0
     let SUBJECT_COUNT=${SUBJECT_COUNT}+1
     SUBJECT_T1_IMAGE=${ANATOMICAL_IMAGES[$i]}
     let k=$i+$NUMBER_OF_MODALITIES