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PennLINC / aslprep

Preprocessing of arterial spin labeling (ASL) data
https://aslprep.readthedocs.io
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Allow `init_asl_std_trans_wf` to accept flexible set of native-space inputs to warp #340

Closed tsalo closed 12 months ago

tsalo commented 1 year ago

Summary

The main difference between ASLPrep's init_asl_std_trans_wf and fMRIPrep's init_bold_std_trans_wf is the list of native-space files to warp to standard space. ASLPrep has ASL versions of many of the same files (bold_aparc, bold_aseg, bold_mask, bold_split), but it also has a bunch of CBF outputs to warp as well. fMRIPrep has t2star instead.

If the workflow could ingest multiple native-space inputs without having to specify them in the function, then ASLPrep could directly use fMRIPrep's function (perhaps moved to niworkflows?).

tsalo commented 1 year ago

One additional difference is that init_asl_std_trans_wf calls the ASL reference workflow, which in turn uses aslcontext.

tsalo commented 1 year ago

I can't do what I'm doing in #341 (i.e., run the workflow and just apply the transforms separately, plus call the reference workflow separately) because the aslref-to-std workflow is more complicated than the aslref-to-t1w workflow (e.g., has to deal with multiple requested standard spaces, has to grab the templates for the standard spaces). I think maybe modifying the fMRIPrep workflow is the only way to go here. Then I could call the reference workflow separately.