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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Update LongReconAll to separate base template id.
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@l-espana
l-espana committed Dec 2, 2022
commit 0b51c5445a222599042fe66a17a7bc45394f6ae4
23 changes: 15 additions & 8 deletions nipype/interfaces/freesurfer/longitudinal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -353,12 +353,18 @@ def cmdline(self):

class LongReconAllInputSpec(ReconAllInputSpec):
subject_id = traits.Str(argstr="-subjid %s", desc="subject name")
long_id = traits.Tuple(
traits.Str(),
traits.Str(),
argstr="-long %s %s",
desc="longitudinal name followed by base template name",
xor=["subject_id"]
long_id = traits.Str(
argstr="-long %s",
desc="longitudinal session/timepoint id",
xor=["subject_id"],
requires=["base_id"],
position=1
)
base_id = traits.Str(
argstr="%s",
desc="longitudinal base template id",
requires=["long_id"],
position=2
)


Expand All @@ -376,11 +382,12 @@ class LongReconAll(CommandLine):

>>> from nipype.interfaces.freesurfer.longitudinal import LongReconAll
>>> longrecon = LongReconAll()
>>> longrecon.inputs.long_id = ("ses-1","sub-template")
>>> longrecon.inputs.long_id = "ses-1"
>>> longrecon.inputs.base_id = "sub-template"
>>> longrecon.inputs.directive = "all"
>>> longrecon.inputs.subjects_dir = "."
>>> longrecon.cmdline
'recon-all -all -long ses-1 sub-template -sd .'
'recon-all -all -long ses-1 -base sub-template -sd .'
"""

_cmd = "recon-all"
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