lesion + brain mask for moving image in registration; mean for 2 iterations...

lesion + brain mask for moving image in registration; mean for 2 iterations and median for all following iterations; additional iteration 7

run_template_construction.py

@@ -1694,9 +1694,9 @@ if __name__ == "__main__":
 
 # Averaging transformed T1 brain images in template space
                 if step < 3:
-                    mod = 'median'
+                    averaging_method = 'median'
                 else:
-                    mod = 'mean'
+                    averaging_method = 'mean'
 
                 if mod['T1_brain_key'] is not None:
                     task_count += 1
@@ -1707,7 +1707,7 @@ if __name__ == "__main__":
                         img_paths.append(tree.get('warped_T1brain'))
                     nln_template_path = tree.get('T1_brain_nln_template')
 
-                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, mod, False), tmp_dir=script_dir,
+                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, averaging_method, False), tmp_dir=script_dir,
                                          kwargs=None, clean="never")
                     # job_ids[44] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[37]])
                     job_ids[44] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[37]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
@@ -1723,7 +1723,7 @@ if __name__ == "__main__":
                         img_paths.append(tree.get('warped_T1head'))
                     nln_template_path = tree.get('T1_head_nln_template')
 
-                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, mod, False), tmp_dir=script_dir,
+                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, averaging_method, False), tmp_dir=script_dir,
                                          kwargs=None, clean="never")
                     # job_ids[45] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[39]])
                     job_ids[45] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[39]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
@@ -1739,7 +1739,7 @@ if __name__ == "__main__":
                         img_paths.append(tree.get('warped_T2head'))
                     nln_template_path = tree.get('T2_head_nln_template')
 
-                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, mod, False), tmp_dir=script_dir,
+                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, averaging_method, False), tmp_dir=script_dir,
                                          kwargs=None, clean="never")
                     # job_ids[46] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[40]])
                     job_ids[46] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[40]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
@@ -1755,7 +1755,7 @@ if __name__ == "__main__":
                         img_paths.append(tree.get('warped_DTIscalar'))
                     nln_template_path = tree.get('DTI_nln_template')
 
-                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, mod, False), tmp_dir=script_dir,
+                    jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, averaging_method, False), tmp_dir=script_dir,
                                          kwargs=None, clean="never")
                     # job_ids[47] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[42]])
                     job_ids[47] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[42]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)