new weighted mask

run_template_construction.py

@@ -1186,7 +1186,7 @@ if __name__ == "__main__":
             print('submitted: ' + task_name)
 
             task_name = '{:03d}_affT_create_weighted_brain_mask'.format(task_count)
-            jobcmd = 'fslmaths ' + aff_template_path + ' -bin -mul 7 -add 1 -inm 1 ' + tree.get('T1_brain_mask_weighted_affine_template')
+            jobcmd = 'fslmaths ' + aff_template_path + ' -thr 0.1 -bin -mul 7 -add 1 -inm 1 ' + tree.get('T1_brain_mask_weighted_affine_template')
             job_ids[23] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[22]])
             # job_ids[23] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[22]], array_task=False)
             print('submitted: ' + task_name)
@@ -1735,7 +1735,7 @@ if __name__ == "__main__":
 
                 task_count += 1
                 task_name = '{:03d}_nlnT_average_T1_brain_mask_weighted'.format(task_count)
-                jobcmd = 'fslmaths ' + nln_template_path + ' -bin -mul 7 -add 1 -inm 1 ' + tree.get(
+                jobcmd = 'fslmaths ' + nln_template_path + ' -thr 0.1 -bin -mul 7 -add 1 -inm 1 ' + tree.get(
                     'T1_brain_mask_weighted_nln_template')
                 job_ids[50] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[49]])
                 # job_ids[50] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[49]], array_task=False)