Hello,

Okay, thanks for the explanation. Is that thickness referring to the cortical thickness?

Eva -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 29 August 2017 15:40 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: EXT: Re: [Freesurfer] Cortical thickness map

thickness isn't a surface - it's a scalar overlay over the surface. Try something like:

freeview -f lh.inflated:overlay=lh.thickness

with the appropriate paths to the surfaces and thickness files

cheers Bruce On Tue, 29 Aug 2017, Esteban, Eva(GE Healthcare) wrote:

Hello everyone,

I am trying to overlay a cortical thickness map onto a subject but when I try this command

freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.thickness.fsaverage.mgh:edgecolor=blue

or this command: freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.thickness:edgecolor=blue

I get an error saying:

nquads=1966084,  nvertices=599

ERROR: MRISread: file '/home/eva/Downloads/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/lh.thickness' has many more faces than vertices!

Probably trying to use a scalar data file as a surface!

Do any of you know how to load it properly?

Thank you!