I am trying to segment the cortex of my subjects into multiple layers and am trying several approaches.

I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and it works perfectly.

I am also interested in trying other approaches from other software packages and have started to experiment with nighres.

Is it possible to convert the FreeSurfer surface files (pial and white) to a nibabel SpatialImage format or another format that can be read by the nibabel/nighres python library?

I have searched the FreeSurfer documentation but couldn’t find a direct answer. I also see that nibabel has a freesurfer module and hence I am able to load the images to a python script. However, when I attempt to use perform volumetric layering with nighres, it returns a value error, given that the “input volume must be either a path to a file that Nibabel can load or a nibabel SpatialImage."

I will also contact the nighres developers but was wondering if Freesurfer already takes into account the possible interaction between different software packages.

Many thanks!

Best regards,

Inês Pereira