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Dear Freesurfer experts,

I have a similar problem as what was mentioned previously on this support list.

I ran recon-all on all of my subjects and I am currently in the manual editing process. I noticed that for a lot of my subjects there are spots in the images where the white matter extends into the gray matter. So its looks like a systematic error with my data. I attached images of two different subjects as an example. I found the advice to change the intensity bounds parameters for mri_segment and mris_make_surfaces, but I don t know exactly how to do this. I am very new to freesurfer and I could not find the proper information on the freesurfer_wiki websites for recon-all, mri_segment and mris_make_surfaces.

1) What is exactly the parameter that I would need to change in mri_segment and mris_make_surfaces? 2) What is the recon-all command that I would need to run to change those default parameters after I made already manual changes to the brain mask (removing voxels) and added control points?

Thank you very much in advance

Our Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

we run it on Linux, kernel version 4.15.0-46-generic, Ubuntu 18.04.1 LTS

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