AFNI interfaces output: default to nifti

[rmarkello]

@Shotgunosine and I have been working on updating and adding various AFNI interfaces, and just finished talking about how to deal with one of the main issues that we've found in all of them: AFNI defaults to outputting BRIK/HEAD files. Because these files have an "orientation tag," (e.g., out_file+orig.BRIK) they are incompatible with traditional implicit out_file naming (i.e., using name_source and name_template). Indeed, most of the existing AFNI Interfaces don't appropriately collect implicitly named output files due to this issue.

We are suggesting coercing all AFNI interface image outputs to default to nifti format (i.e., as is currently done with FSL Interfaces). @Shotgunosine has spoken with the AFNI team at the NIMH who reported that they didn't foresee any issues with this. However, since this change would affect all existing AFNI interfaces, we thought it best to post about it here for discussion before implementing anything.

We hope to follow up on this implementation by create an AFNIImage class to permit nifti sub-brick selection (see: sub-brick selection).

[wizofe]

Interesting issue raised here and even more that's revisited after 5 years. I am trying to incorporate AFNI's DegreeCentrality in one of my pipelines. It seems that there's no support for sub-brick selection, which is quite important as AFNI by default is outputting a binary degree centrality (rather than weighted which is stored inside the second sub-brick).

Any ideas on how I could choose that as my output? Or how this can be implemented in nipype?

Thank you!