Tim Coalson

I have other things to work on, please proceed. You might want to write a test of "is this file a label volume", using `wb_command -file-information -no-map-info`, and use it...

If the SE fieldmaps and the BOLD have the same orientation before the reorient2std, then the same axis flips/swaps apply to both. If they are only flips, then something like...

My thought on the recent error is that someone misunderstood the description of that argument (which contains a slash that I think is intended to indicate "or", considering the logic...

These options sound like they are intended to provide what would have been the level 2 information, so that the directory structure will match what doing the level 2 mode...

If it really is as simple as "the same information, used a different way", it could be less confusing to explain to users than "here are different flags that must...

https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/IcaFixProcessingBatch.sh might help. Note that you need to have run the earlier pipelines on your data already (all three freesurfer ones, and fMRI volume and surface).

## Story 18: Correspondence to MRI coordinates (related to 4, 5, 12, and 15, but with details from our existing wb_view implementation) 1. User collects T1w and other MRI scans...

Just a comment - from an outside perspective (I work mostly with MRI), the prospect of having the transform and blending stage of stitching happening on the fly during display...

Do we know how the VN file ended up with 0s where the data isn't 0?

If the FoV is missing something in the BOLD scan, wouldn't that result in 0 values in that location (possibly dilated into at some point, but that wouldn't have 0...