I'm trying to calculate the local gyrification index for the test subject Bert (or any of my own subjects for that matter) but I'm running into an error when FS tries to read the lh.pial surface.  

I have the exact same error as Louise (see: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050593.html) but that doesn't seemed to have been answered yet. 

The error basicly takes place during the FS matlab command freesurfer_read_surf, where it is unable to read the lh.pial (see the log). This also causes the command find_corresponding_center_FSformat to fail because there are no faces/vertices as input. 

">> FREESURFER_READ_SURF [v  1.2 ]

Error using freesurfer_read_surf (line 90)

could not open surface file lh.pial.

Error in find_corresponding_center_FSformat (line 26)

[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);"

If I run freesurfer_read_surf directly from matlab with the lh.pial as input, it does return the faces/vertices to me in my matlab workspace. This led me to think there might be a communication error between the FS toolbox and matlab itself (or maybe the lh.pial is specified incorrectly?). 

Am I missing something here? 

FS versions used: nightly build and stable 6.0

Matlab version: 2017a

OS: ubuntu 16.04

uname -a: Linux michael-M11AD 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Cheers,

Michael