Re: [Freesurfer] issues with -T2pial option in v.5.3

Dear Petr, according to the screenshot, the problem is that there is quite low signal intensity in the cut-out parts of gray matter on T2 images. Apart from HCP pipelines, you can try to increase -nsigma_below parameter of mris_make_surfaces to prevent this cut-out. The default value is 3, try

Re: [Freesurfer] issues with -T2pial option in v.5.3

You could try with the HCP Pipelines and see if that helps: https://github.com/Washington-University/Pipelines Peace, Matt. From: on behalf of Petr Bednarik Reply-To: Freesurfer support list Date: