[Neuroimaging] [fmriprep] Specifying different priors and templates

[Dan Lurie]

Hey fmriprep team,

I am working on a pull request to add support for using lesion masks during
T1 registration, and wanted to check in with you guys before I got too
deep. A couple of questions:

1) I’m assuming it’s best to create a separate new pipeline based on ds005
instead of modifying ds005? I want to make sure i’m adding things in a way
that is consistent with the overall architecture you’ve envisioned.

2) Lesion masks are usually in subject native space, so using cost function
masking in ANTs requires specifying the template as the moving image and
then using the inverse transforms (see here:
https://github.com/stnava/ANTs/issues/48). My plan was to just change the
pipeline workflow inputs/outputs to accommodate this change (e.g. use the
inverse transform when registering the EPI and TPMs). Is there anything
tricky about how the pipeline is organized that I should keep in mind when
doing this?

3) is run_workflow.py the place to add options/settings for things like
specifying what templates to use during skull stripping and tissue
segmentation? I looked through the BIDS-Apps docs to see if there was any
common design pattern established, but didn’t see anything.

Thanks in advance, and apologies if I’m missing anything obvious. Happy to
chat over Skype/Hangouts if that’s easier than email.
Dan

-- 
Dan Lurie
Graduate Student
Department of Psychology
University of California, Berkeley
http://despolab.berkeley.edu/lurie
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