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backport fix copy of dseg.tsv following templateflow update for LTS #421

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backport fix copy of dseg.tsv following templateflow update for LTS #421

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4 changes: 3 additions & 1 deletion smriprep/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,7 +247,9 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None):
if opts.run_reconall:
from templateflow import api
from niworkflows.utils.misc import _copy_any
dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
dseg_tsv = str(
api.get('fsaverage', hemi=None, atlas=None, suffix='dseg', extension=['.tsv'])
)
_copy_any(dseg_tsv,
str(Path(output_dir) / 'smriprep' / 'desc-aseg_dseg.tsv'))
_copy_any(dseg_tsv,
Comment on lines +250 to 255
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We'll need an associated PR against the fMRIPrep LTS branch. At least the Docker container pins the specific templateflow version, so this line either needs to be one that works for versions 0.7.1 and 24.1.0 or we'll need to check the version.

https://github.com/nipreps/fmriprep/blob/maint/20.2.x/docker/files/environment.yml#L202

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Given that the valid query parameters changed in 24.1, I don't think we can do this reliably across versions with a single command. I would suggest for the LTS:

dseg_LUTs = api.get(OLD_PARAMS)
if isinstance(dseg_LUTs, list):
    dseg_LUTs = api.get(NEW_PARAMS)  # Requires tf 24.1+
if isinstance(dseg_LUTs, list):
    dseg_LUTs = dseg_LUTs[0]
dseg_tsv = str(dseg_LUTs)

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