Orientation error in norm.py create_cfm (Create a mask to constrain registration.).

[rbakker]

What happened?

In this routine, two volumes are combined, one (the lesion mask) has its voxels reoriented to RAS orientation (line 553 lm_img = nb.as_closest_canonical(nb.load(lesion_mask)), the other volume (in_file) is left untouched. So it both have voxel orientation LPS to start with, we are subtracting reoriented voxels from non-reoriented voxels, which is wrong.

What command did you use?

create_cfm in norm.py

What version of the software are you running?

master branch

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Additional information / screenshots

No response