Commit 4d0f1da2 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

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
parent 18c307ff
......@@ -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)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment