Tim Coalson

I expect once the course is done and things have calmed down, and the command-building code is fully generic, we can copy the missing comments into the generic version, replace...

Where is some data that we can look at? In the HCA data in ceph, this file appears to be written by FSL, with no XML extension that could contain...

That looks like it was still written by FSL, but FSL 6.0.5 may be blindly copying extensions from the input volume, while 6.0.1 discarded them.

Yes, I had also just found that the extension was being copied from the reference, not the input data file.

We don't have a dedicated command for stripping extensions, but `wb_command -volume-math 'x' -var x brainmask_fs.2.nii.gz brainmask_fs.2.nii.gz` should get the job done.

Alternatively, `wb_command -volume-resample` should be able to replace the core features of `applywarp`, but only exists starting with 1.5.0.

In this case, though, there isn't even a transform in the resampling, so `wb_command -volume-affine-resample` with the identity matrix should work, which is much older (specifically, works for our specific...

That is probably the approach that is least likely to change what voxels are "on" in the mask. We should check for other applywarp commands that use the Atlas_ROIs file...

Yes, -volume-label-import ignores the label table of the input file. Structural images will display very wrong with label rendering. It would probably show colors in the background noise where the...

I think the only wb_commands that specifically round their output values based on the assumptions of writing label data have "label" in their name, so the internal values of the...