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Support predefined goodvoxels mask in init_bold_fsLR_resampling_wf #3169

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tsalo opened this issue Dec 4, 2023 · 2 comments · Fixed by #3170
Closed

Support predefined goodvoxels mask in init_bold_fsLR_resampling_wf #3169

tsalo opened this issue Dec 4, 2023 · 2 comments · Fixed by #3170
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CIFTI / Grayordinates

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@tsalo
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tsalo commented Dec 4, 2023

What would you like to see added in fMRIPrep?

I am currently using fMRIPrep as a dependency for ASLPrep, and, while the currently version of init_bold_fsLR_resampling_wf allows me to convert preprocessed ASL files to CIFTIs, I can't use the goodvoxels mask generated from the ASL file when converting derived CBF maps to CIFTIs.

It might even be worth it to move init_bold_fsLR_resampling_wf to niworkflows, since it's useful beyond just BOLD data.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

This might be useful for PET as well (I'm not sure what PET processing looks like).
@effigies
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effigies commented Dec 4, 2023

So from the perspective of the workflow, we would be passing a volume_roi to the volume_to_surface node, and the input would change from bold_file to in_file. Goodvoxels would be run separately to provide input.

That seems fine to port a version of that over to niworkflows. We can adopt it here once it's in a release. Should be a pretty minor refactor.

@mnoergaard Would there be a PET use for resampling volumes to fsLR grayordinates? Any wrinkles that we should know about?

@tsalo tsalo mentioned this issue Dec 5, 2023
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effigies added a commit that referenced this issue Dec 6, 2023
@effigies
Separate goodvoxels mask creation from fsLR resampling (#3170)
5f332e8 
Closes #3169. This could just be a first step toward moving one or more of these workflows from fMRIPrep to niworkflows.


- Move `init_goodvoxels_bold_mask_wf` call out of `init_bold_fsLR_resampling_wf`. This will allow downstream tools (e.g., ASLPrep) to generate the goodvoxels mask from one file (the ASL time series) and apply it to others (e.g., CBF maps).
- Clean up `init_bold_fsLR_resampling_wf` (e.g., remove unused imports and add all parameters to docstring).
- Move BOLD-to-anatomical resampling workflow call from `resampling` level to `full` level, since it doesn't produce any outputs.
@mnoergaard
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Yes - there will be a PET use for resampling volumes to fsLR grayordinates. But no wrinkles :-)

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Separate goodvoxels mask creation from fsLR resampling tsalo/fmriprep
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@effigies @tsalo @mnoergaard