Hi Bruce,
Thanks so much for your response. It was exactly what I was looking for.
My next question has to do with the process of projecting fractional anisotropy data onto the new interior white surface, followed by taking the mean FA within a lobe or individual parcellation. I used mri_surf2vol (command line below) to create a binary mask of the voxels that intersect the white surface (i.e. -2mm from the gray/white boundary) then applied this mask to my FA data. Is this process ok or should I use mri_vol2surf(not too familiar with this tool)? Let me know if I've veered off into a wrong direction.
mri_surf2vol --mkmask --surf white-2mm --hemi lh --identity subj --template ./subj/mri/lh.white.fill.mgz --o ./subj/mri/lh.white-2mm.surfMask.mgz
lh.white.fill.mgz is a binary mask of the lh.white surface (GM?WM boundary) created using mris_fill.
Thanks! -Jason
On 06/19/2013 10:39 AM, Bruce Fischl wrote:
Hi Jason
you could try using mris_expand with a negative # of millimeters. At 4mm you will lose a lot of the gyri and the procedure will probably fail, but for smaller amounts it should work (and is what we've done in the past). You can also use mris_distance_transform to compute the distance transform for the wm and use negative distances to find the distance into the interior
cheers Bruce
On Wed, 19 Jun 2013, Jason Reed wrote:
Dear FreeSurfer Experts,
I am attempting to construct surfaces that are 1, 2, 3, and 4 mm interior from the GM/WM boundary (?h.white). So going gradually deeper into white matter from the GM/WM boundary. I have successfully used mris_fill to fill the ?h.white surface and mri_morphology to erode the resulting volume, but I'm not sure on the correct procedure to create the new surfaces. Any advice or suggestions on tools with options to use will be greatly appreciated!
My eventual goal is to project coregistered DTI data onto these more interior white matter surfaces.
Thanks! -Jason
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