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[ENH] Issue 3345: Adding FreeSurfer longitudinal interfaces #3529

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Merged
merged 18 commits into from
Jul 5, 2023
Merged

[ENH] Issue 3345: Adding FreeSurfer longitudinal interfaces #3529

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da35d17
Initial addition of FreeSurfer longitudinal interfaces.
l-espana Nov 29, 2022
d6ec3bd
Style and testing.
l-espana Nov 29, 2022
0b51c54
Update LongReconAll to separate base template id.
l-espana Dec 2, 2022
6a294be
Forgot check-before-commit. Update LongReconAll docstring.
l-espana Dec 2, 2022
6971865
Update longitudinal outputs to match separation of ids.
l-espana Dec 14, 2022
2d2072f
Update/fix zenodo.
l-espana Dec 14, 2022
d38e98f
Remove subject_id input per code review
l-espana Dec 15, 2022
725cd82
Make base recon inputs more explicit per code review
l-espana Dec 15, 2022
7d5253e
Make longitudinal recon more explicit per code review
l-espana Dec 15, 2022
bdc39fc
Fix typo
l-espana Dec 15, 2022
78a5feb
Refactor longitudinal pipeline to live within ReconAll interface.
l-espana Dec 28, 2022
c82b279
Black formatting.
l-espana Dec 28, 2022
c52cf92
Fix list_outputs typo.
l-espana Jan 4, 2023
262bfb4
Additional xor/requires constraints
l-espana Apr 12, 2023
46e07bb
Apply formatting suggestions from code review
l-espana Apr 14, 2023
123ac53
Merge branch 'master' into iss3345
effigies Jul 5, 2023
34a4ac6
STY: Run black and fix typo
effigies Jul 5, 2023
78d580b
TEST: make specs
effigies Jul 5, 2023
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5 changes: 5 additions & 0 deletions .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -890,6 +890,11 @@
"affiliation": "MIT, HMS",
"name": "Ghosh, Satrajit",
"orcid": "0000-0002-5312-6729"
},
{
"affiliation": "Department of Neurosurgery, Medical College of Wisconsin",
"name": "Espana, Lezlie",
"orcid": "0000-0002-6466-4653"
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I'd suggest to modify the zenodo file within its own commit. Also, I believe you should keep Satra as last author.

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Oh of course, my mistake.

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No problem

}
],
"keywords": [
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4 changes: 2 additions & 2 deletions nipype/interfaces/freesurfer/longitudinal.py
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Expand Up @@ -405,7 +405,7 @@ def _gen_filename(self, name):
return None

def _list_outputs(self):
subject_id = f"{self.inputs.long_id[0]}.long.{self.inputs.long_id[1]}"
subject_id = f"{self.inputs.long_id}.long.{self.inputs.base_id}"

if isdefined(self.inputs.subjects_dir):
subjects_dir = self.inputs.subjects_dir
Expand All @@ -430,7 +430,7 @@ def _list_outputs(self):

def _is_resuming(self):
subjects_dir = self.inputs.subjects_dir
subject_id = f"{self.inputs.long_id[0]}.long{self.inputs.long_id[1]}"
subject_id = f"{self.inputs.long_id}.long{self.inputs.base_id}"
if not isdefined(subjects_dir):
subjects_dir = self._gen_subjects_dir()
if os.path.isdir(os.path.join(subjects_dir, subject_id, "mri")):
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