Commit 2921252d authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

intensity normalisation before averaging

parent 176c9696
......@@ -32,10 +32,6 @@ def writeConfig(step,mod,fpath):
"""
# For future use of individual subject masks:
# use_mask_mov_scalar
# use_mask_mov_tensor
T1_head = True if mod['T1_head_key'] is not None else False
T2_head = True if mod['T2_head_key'] is not None else False
DTI = True if mod['DTI_tensor_key'] is not None else False
......@@ -425,8 +421,8 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
@param log_dir: Directory where output log-files will be saved
@param queue: Name of queue to submit the job to
@param wait_for: List of IDs of jobs required to finish before running this job.
@param script: Function can take path to a shell script, which contains one command per line - commands will be submitted as an array job
@param command: Alternatively function can take a command as a string - command will be submitted as single job
@param script: Path to a shell script, which contains one command per line - commands will be submitted as an array job
@param command: Alternatively a single command can be provided as a string - command will be submitted as single job
@param coprocessor_class: Coprocessor class, if not None cuda will be selected
@param export_var: Environment variables to be exported to the submission node
@param debug: If True, information about job will be written to output
......@@ -1463,7 +1459,7 @@ if __name__ == "__main__":
warped_path = tree.get('warped_T1brain')
warp_path = tree.get('mmorf_warp_resampled_unbiased_full_T1brain')
jobcmd = func_to_cmd(applyWarpWrapper, args=(
img_path, img_ref_T1head_path, warped_path, warp_path, 'spline', True),
img_path, img_ref_T1head_path, warped_path, warp_path, 'spline', False),
tmp_dir=script_dir, kwargs=None, clean="never")
f.write(jobcmd + '\n')
job_ids[37] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=cpuq,
......@@ -1481,7 +1477,7 @@ if __name__ == "__main__":
warped_path = tree.get('warped_T1brain_mask')
warp_path = tree.get('mmorf_warp_resampled_unbiased_full_T1brain')
jobcmd = func_to_cmd(applyWarpWrapper,
args=(img_path, img_ref_T1head_path, warped_path, warp_path, 'nn', True),
args=(img_path, img_ref_T1head_path, warped_path, warp_path, 'nn', False),
tmp_dir=script_dir, kwargs=None, clean="never")
f.write(jobcmd + '\n')
job_ids[38] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=cpuq,
......@@ -1504,7 +1500,7 @@ if __name__ == "__main__":
warped_path = tree.get('warped_T1head')
warp_path = tree.get('mmorf_warp_resampled_unbiased_full_T1head')
jobcmd = func_to_cmd(applyWarpWrapper, args=(
img_path, img_ref_T1head_path, warped_path, warp_path, 'spline', True),
img_path, img_ref_T1head_path, warped_path, warp_path, 'spline', False),
tmp_dir=script_dir, kwargs=None, clean="never")
f.write(jobcmd + '\n')
job_ids[39] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=cpuq,
......@@ -1523,7 +1519,7 @@ if __name__ == "__main__":
warped_path = tree.get('warped_T2head')
warp_path = tree.get('mmorf_warp_resampled_unbiased_full_T2')
jobcmd = func_to_cmd(applyWarpWrapper, args=(
img_path, img_ref_T1head_path, warped_path, warp_path, 'spline', True),
img_path, img_ref_T1head_path, warped_path, warp_path, 'spline', False),
tmp_dir=script_dir, kwargs=None, clean="never")
f.write(jobcmd + '\n')
job_ids[40] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=cpuq,
......
Markdown is supported
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