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Track sources with DatasetLinks and BIDS-URIs #3252

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tsalo opened this issue Mar 9, 2024 · 4 comments · Fixed by #3255 or #3297
Closed

Track sources with DatasetLinks and BIDS-URIs #3252

tsalo opened this issue Mar 9, 2024 · 4 comments · Fixed by #3255 or #3297
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BIDS feature

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@tsalo
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tsalo commented Mar 9, 2024

What would you like to see added in fMRIPrep?

I was thinking it would be nice to output Sources metadata fields for all outputs, using DatasetLinks and BIDS URIs to track the files.

DatasetLinks and BIDS URIs were added in 1.8.0, so we would need to increase the BIDSVersion to at least 1.8.0.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

I've had some success doing this in XCP-D, and I think it would be even easier in fMRIPrep since we could put a DatasetLinks field in the Config object.
@tsalo tsalo mentioned this issue Mar 11, 2024
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effigies pushed a commit that referenced this issue Mar 22, 2024
@tsalo @mgxd
ENH: Use BIDS URIs to track Sources in sidecars (#3255)
6f8c965 
Closes #3252. This is just a first pass- it only modifies the RawSources
for now. I can add the immediate Sources in another PR (this'll require
a lot more effort).

## Changes proposed in this pull request

- Add `DatasetLinks` field to the `dataset_description.json`
    - The input dataset is called `raw`
- Any other datasets supplied through `--derivatives` are automatically
named `deriv-<index>`. We might want to support named derivatives at
some point.
- Replace BIDS-relative paths in `RawSources` fields with BIDS-URIs.
- Change `RawSources` to `Sources` in the sidecar files, since
`RawSources` is deprecated.

## Documentation that should be reviewed

I'll probably need to update the documentation, but haven't yet.

---------

Co-authored-by: Mathias Goncalves <goncalves.mathias@gmail.com>
@tsalo tsalo mentioned this issue Mar 25, 2024
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@effigies
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effigies commented Jun 4, 2024

@tsalo Could you redo #3255 with the latest changes in #3292 merged into master? I didn't want to try to do it in a merge commit.

@effigies effigies reopened this Jun 4, 2024
@tsalo
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tsalo commented Jun 4, 2024

Sorry, I'm a little confused. It doesn't look like the changes in #3255 were reverted in master when you merged in #3292. Am I missing something?

@effigies
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effigies commented Jun 4, 2024 •
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The ds_boldmask_wf workflow that got pulled out in maint/23.2.x still has RawSources. When I merged the latest release into master (2e863b7), I did not try to merge it as if you had split the workflow out from the current state of master.

@tsalo
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tsalo commented Jun 4, 2024

Ohhh okay. I'll take a look at that then.

@tsalo tsalo mentioned this issue Jun 4, 2024
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effigies pushed a commit that referenced this issue Jun 4, 2024
@tsalo
Use BIDSURI in init_ds_boldmask_wf (#3297)
604eeef 
Closes #3252.

## Changes proposed in this pull request

- Replace `RawSources` in `init_ds_boldmask_wf` with `Sources`
determined using `BIDSURI`.
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