Problem with cat12 - creates cube shaped head mask

Bugs
1

Hi,
I'm having a problem with CAT12 segmentation, where the head mask comes out as a cube. The brain inside is fine but I can't use the head for source reconstruction.

Interestingly, this has only happened for 2 out of 10+ MRI scans with the same acquisition settings. I have followed this up with the MRI team and nothing seems to be wrong with the acquisition - the tech was able to use CAT12 without an issue (outside of brainstorm).

I haven't been able to understand why this is happening. The only thing I note is that the scan is a bit dark, but the contrast seems to be fine.

Do you have any tips?
Thank you!

image
image1221×1107 68.5 KB

2

image
image522×537 35 KB

3

The head surface is generated by Brainstorm, not by CAT12.

First, check that the outputs of CAT12 are correct: Open the cortex surface and the volume atlases to make sure the segmentation worked correctly.

Then try to recompute a different head surface from the MRI, following the instructions on that page:
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#The_head_surface_looks_bad