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ftdc-picsl / pmacsBrainExtraction

Wrappers to manage brain extraction tools
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Conform data to standard space with c3d -swapdim #1

Closed cookpa closed 11 months ago

cookpa commented 11 months ago

Need to figure out what code to use (I think RPI, that's what c3d reports for the FSL MNI template)

cookpa commented 11 months ago

I think preps use nipype for this

https://nipype.readthedocs.io/en/1.4.0/interfaces/generated/nipype.interfaces.image.html

cookpa commented 11 months ago

Looks like it won't be an issue for most data because dcm2niix does this automatically - done explicitly in T1wPreprocessing repo just in case