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Track immediate Sources
when possible
#3261
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References #3261. ## Changes proposed in this pull request - Track `Sources` for standard-space outputs --------- Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@effigies do you think it would be worth it to try incorporating the TemplateFlow templates into the DatasetLinks and Sources? |
Related to #3261. ## Changes proposed in this pull request - Add an outputnode to `init_ds_volumes_wf` with the saved `bold` path. - Add `sources` field to `init_bold_surf_wf`'s inputnode. - Infer Sources for functional GIFTI outputs. - If the user has requested T1w-space outputs, then this should be `bold` from the associated `ds_volumes_wf` and `fsnative2t1w_xfm` - If the user didn't want T1w-space volumetric outputs, then this should be the raw BOLD file, `motion_xfm`, `boldref2anat_xfm`, `fsnative2t1w_xfm`.
Yes, I think including templateflow would be very helpful both for sources and spatial references. |
Want to note that
|
Each of these is an atomic transform. orig-to-boldref + boldref-T1w are strung together to get the individual volume there, but boldref-to-fmap is used to transform the fieldmap into the boldref space and calculate a voxel-shift-map. We do not save the VSM, so it would be appropriate to include both the fieldmap and the transform as inputs. The exact provenance would be better modeled using |
Ah, thanks! I think SDCFlows will need to pass its fmap file from its derivatives workflow in order to use it as a source in fMRIPrep. |
References #3261. ## Changes proposed in this pull request - Add the TemplateFlow base directory to the DatasetLinks. - Add the template used for normalization to the Sources for standard-space volumetric outputs.
What would you like to see added in fMRIPrep?
Sources
.Sources
should probably be the boldref-space outputs, when those are requested. Otherwise, they should include the original data, the HMC transforms, the coreg transforms, the ref2anat transform, and the anat2std transform.Sources
.Sources
), so we need to compile themeta_dict
beforehand. This has come up a lot in XCP-D, so I've been working on an interface that can handle it (see GenerateMetadata in Add BIDSURI and GenerateMetadata interfaces to track Sources PennLINC/xcp_d#1104).Sources
.Do you have any interest in helping implement the feature?
Yes
Additional information / screenshots
No response
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