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Correct vbm longitudinal #54

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Merged
AGrigis merged 2 commits into from
Apr 22, 2026
Merged

Correct vbm longitudinal #54

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0be3660
brainprep/interfaces/cat12: create session folders in longitudinal vbm
AymericGaudin Apr 21, 2026
18cf5d2
brainprep/interfaces/cat12: Look for the right output files in the lo…
AymericGaudin Apr 21, 2026
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10 changes: 9 additions & 1 deletion brainprep/interfaces/cat12.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@ def cat12vbm_wf(
cat12_file = opts.get("cat12_file", DEFAULT_OPTIONS["cat12_file"])
spm12_dir = opts.get("spm12_dir", DEFAULT_OPTIONS["spm12_dir"])
matlab_dir = opts.get("matlab_dir", DEFAULT_OPTIONS["matlab_dir"])
longitudinal = len(t1_files) > 1

output_dirs = [
output_dir / f"ses-{info['ses']}"
Expand All @@ -101,6 +102,11 @@ def cat12vbm_wf(
f"catreport_{im_file.name.replace('nii.gz', 'pdf')}"
for im_file, trg_dir in zip(t1_files, output_dirs, strict=True)
]
if longitudinal:
gm_files = [Path(str(filepath).replace("mwp1", "mwp1r"))
for filepath in gm_files]
qc_files = [Path(str(filepath).replace("catreport_", "catreport_r"))
for filepath in qc_files]

command = [
str(cat12_file),
Expand Down Expand Up @@ -180,7 +186,6 @@ def write_catbatch(
f"ses-{entities[0]['ses']}" /
f"cat12vbm_matlabbatch_run-{entities[0]['run']}.m"
)
batch_file.parent.mkdir(parents=True, exist_ok=True)
template_batch = (
Path(__file__).parent.parent /
"resources" /
Expand All @@ -190,6 +195,9 @@ def write_catbatch(
output_dir / f"ses-{info['ses']}"
for info in entities
]
batch_file.parent.mkdir(parents=True, exist_ok=True)
for output_dir in output_dirs:
output_dir.mkdir(exist_ok=True)
unzip_t1_files = [
trg_dir / im_file.name.replace(".gz", "")
for im_file, trg_dir in zip(t1_files, output_dirs, strict=True)
Expand Down
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