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Fix subject_id formatting in run_hippunfold_parallel #14

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Fix subject_id formatting in run_hippunfold_parallel #14

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faa1907
Fix subject_id formatting in run_hippunfold_parallel
ckronlage Oct 3, 2025
fda1e1c
Add checks before deleting intermediate files in run_hippunfold_parallel
ckronlage Oct 15, 2025
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9 changes: 6 additions & 3 deletions scripts/preprocess/run_script_segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@ def run_hippunfold_parallel(subjects, bids_dir=None, hippo_dir=None, num_procs=1

if subjects_to_run!=[]:
print(get_m(f'Start Hippunfold segmentation in parallel for {subjects_to_run}', None, 'INFO'))
command = format(f"hippunfold {bids_dir} {hippo_dir} participant --participant-label {' '.join(subjects_to_run)} --core {num_procs} --modality T1w")
subjects_to_run_shortformat = [subject_id.split('sub-')[-1] for subject_id in subjects_to_run]
command = format(f"hippunfold {bids_dir} {hippo_dir} participant --participant-label {' '.join(subjects_to_run_shortformat)} --core {num_procs} --modality T1w")
if verbose:
print(command)
proc = Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding='utf-8')
Expand All @@ -55,8 +56,10 @@ def run_hippunfold_parallel(subjects, bids_dir=None, hippo_dir=None, num_procs=1
if delete_intermediate:
print(get_m(f'Delete intermediate files that takes lot of space: hippunfold_outputs/hippunfold/<subject_id>/warps and hippunfold_outputs/work folders', subjects_to_run, 'INFO'))
for subject in subjects_to_run:
shutil.rmtree(hippo_dir, 'hippunfold', subject, 'warps')
shutil.rmtree(hippo_dir, 'work', f'{subject}_work.tar.gz')
if os.path.exists(os.path.join(hippo_dir, 'hippunfold', subject, 'warps')):
shutil.rmtree(os.path.join(hippo_dir, 'hippunfold', subject, 'warps'))
if os.path.isfile(os.path.join(hippo_dir, 'work', f'{subject_bids_id}_work.tar.gz')):
os.remove(os.path.join(hippo_dir, 'work', f'{subject_bids_id}_work.tar.gz'))
return True
else:
print(get_m(f'Hippunfold segmentation failed for 1 of the subject. Please check the logs at {hippo_dir}/logs/<subject_id>', None, 'ERROR'))
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