Final bugs squashed.

Tested and working

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