Freesurfers,

I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked).

Code I used:

Mri_mask original_surface_overlay label_mask new_masked_output

 

It doesn’t output any errors.

Here is what it looks like in freeview:

Original surface overlay (label is outlined in green)

The label made into a surface overlay (same  as the one shown in green above):

But this is the output: all zeros even though there was data within the mask.

 

Help!

Sara A. Sims