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Thanks for pointing out the -r option, I hadn't seen that one before in the documentation. It indeed pushed the pial surface to the correct place in some parts of the brain (unfortunately not everywhere). Running mris_make_surfaces with the -noaseg flag did the trick for some reason.

________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Verzonden: zaterdag 14 december 2019 00:07:02 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Spam] Re: [Freesurfer] Pial surface does not follow the gray/csf boundary

It is hard to say. The 0.25mm may be throwing it off. You can try adding -r 0.25. This will increase the force that repels the pial surface from the white by a factor of 10. That might be enough. But there are a lot of places where mris_make_surfaces assumes that the voxels are 1mm. Sometimes people will change the voxel size in the header to 1mm (so no change to the pixel data, just a change to the header) and then run that.

On 12/12/2019 7:07 AM, Ardesch, D.J. wrote:

External Email - Use Caution Dear FreeSurfers,

I’m trying to create surface reconstructions for some small monkey scans (about half the size of a rhesus macaque). The white surfaces look fine, but I can’t seem to get the pial surfaces to extend properly to the edge of the gray matter. Is there a way to ‘force’ the mris_make_surfaces command to place the pial surface along a certain voxel intensity or intensity gradient?

As I understand it, mris_make_surfaces takes the ?h.orig surface and extends it into the gray matter until it finds the gray matter/csf boundary. I’ve therefore tried to edit the brain.finalsurfs.mgz and brainmask.mgz volumes such that all white matter voxels have an intensity of 110 and all other brain voxels have an intensity of 80, and added some smoothing to create an intensity gradient, but this did not make a difference. The gray matter surface is still placed about 1/5th of the way between the gray/white boundary and the gray/csf boundary. Adding a T2 scan did not help either.

My setup is the following:

* FreeSurfer v6.0.0 * MacOS 10.14.6 * Running FreeSurfer with the -hires flag (voxel size is 0.25 mm isotropic)

With some manual editing I’ve been able to complete all pipeline steps until the surface reconstruction, except the topology fixing because it created large inaccuracies in the occipital lobe (including the topology fixing step did not solve the problem either).

Any help would be greatly appreciated!

With kind regards, Dirk Jan

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