[WIP] FIX: Anatomic fast track (except freesurfer/surface rec.) #272
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Hello @nuKs! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2021-11-26 16:27:11 UTC |
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What my patch does is to rely on pybids layout instead of bids build_path in order to retrieve the fast_track derivatives files. Pybids layout does adapt to any bids-valid naming scheme, while build_path does not, but rather directly assumes the file name. So far, examples that make fast-track fails include: - subjects with a single T1 (as the path is different since no template is made) - subjects with T1 containing run-x segments within the name. EXAMPLE: In my case, IBC has been failing (without fix) for some subjects, modified/reduced day2day datasets too. IBC openneuro: https://openneuro.org/datasets/ds002685/versions/1.3.1 day2day upon request: https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0383-y WARNING: This fix is less restrictive than previous version, thus might select too much files. This risk should properly be assessed. WARNING: freesurfer files aren't fixed. cf. nipreps#224
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nuKs
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@oesteban where can I download ds054 (it's not here: https://openfmri.org/dataset/) ? ds054 tests fail while ds005 do not. Might be a problem with my approach (cf. my #224 comments), though I am not sure. |
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If this still needs doing, let's start over from the current master. |
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What my patch does is to rely on pybids layout instead of bids build_path in order to retrieve the fast_track derivatives files.
Pybids layout does adapt to any bids-valid naming scheme, while build_path does not, but rather directly assumes the file name.
So far, examples that make fast-track fails include:
EXAMPLE:
In my case, IBC has been failing (without fix) for some subjects, modified/reduced day2day datasets too.
IBC openneuro: https://openneuro.org/datasets/ds002685/versions/1.3.1
day2day upon request: https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0383-y
WARNING:
This fix is less restrictive than previous version, thus might select too much files.
This risk should properly be assessed.
WARNING:
freesurfer files aren't fixed.
cf. #224