--- a
+++ b/GWR/groupwise_niftyreg_params.sh
@@ -0,0 +1,29 @@
+#!/bin/sh
+
+############################################################################
+###################### PARAMETERS THAT CAN BE CHANGED ######################
+############################################################################
+# Array that contains the input images to create the atlas
+export IMG_INPUT=(`ls /home/arbaza1/scratch/morph_data/Tc1_Nick_TBM_Paper/1.1_FILES/*.nii.gz`)
+export IMG_INPUT_MASK= # leave empty to not use floating masks
+
+# template image to use to initialise the atlas creation
+export TEMPLATE=`ls ${IMG_INPUT[0]}`
+export TEMPLATE_MASK= # leave empty to not use a reference mask
+
+# folder where the result images will be saved
+export RES_FOLDER=`pwd`/groupwise_result_Sba
+
+# argument to use for the affine (reg_aladin)
+export AFFINE_args="-omp 8"
+# argument to use for the non-rigid registration (reg_f3d)
+export NRR_args="-omp 8"
+
+# number of affine loop to perform - Note that the first step is always rigid
+export AFF_IT_NUM=10
+# number of non-rigid loop to perform
+export NRR_IT_NUM=10
+
+# grid engine arguments
+export SBATCH_CMD="sbatch --account=rrg-mfbeg-ad --time=15:30:00 --ntasks=8 --mem-per-cpu=20G --export=ALL --mail-user=arbaza@sfu.ca --mail-type=BEGIN --mail-type=END --mail-type=FAIL --export=ALL --requeue"
+############################################################################