8000 [ENH] Issue 3345: Adding FreeSurfer longitudinal interfaces by l-espana · Pull Request #3529 · nipy/nipype · GitHub
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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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Remove subject_id input per code review 
Co-authored-by: Ghislain Vaillant <ghisvail@users.noreply.github.com>
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@l-espana @ghisvail
l-espana and ghisvail authored Dec 15, 2022
commit d38e98f456940526aa6d35c144b327652ce11173
2 changes: 0 additions & 2 deletions nipype/interfaces/freesurfer/longitudinal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -256,7 +256,6 @@ def _list_outputs(self):


class BaseReconAllInputSpec(ReconAllInputSpec):
subject_id = traits.Str(argstr="-subjid %s", desc="subject name")
base_id = traits.Str(argstr="-base %s", desc="base template name", xor=["subject_id"])
timepoints = InputMultiObject(
traits.Str(), argstr="-tp %s...", desc="processed time point to use in template"
Expand Down Expand Up @@ -352,7 +351,6 @@ def cmdline(self):


class LongReconAllInputSpec(ReconAllInputSpec):
subject_id = traits.Str(argstr="-subjid %s", desc="subject name")
long_id = traits.Str(
argstr="-long %s",
desc="longitudinal session/timepoint id",
Expand Down
0