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Hi Malav, try
mris_diff --min-dist lh.wm.smth5 lh.pial.smth5 1 lh.thickness
The output will be on the pial surface. Reverse the surface order to get
it on the white surface
doug
On 5/22/2023 5:48 AM, Malav Shah wrote:
External Email - Use Caution
Dear freeSurfer team,
I am trying to extract cortical thickness in a postmortem elephant
(structural) MRI scan.
I initiated the process with the segmentation of white (wm) and pial
matter, using MATLAB image processing tools.
Having satisfied white and pial matter labels, I "tesselated" these
volumes to generate pial and wm surfaces.
Then, with 'mris_smooth' command, I smoothed these surfaces.
When attempted to estimate cortical thickness between these surfaces
(lh.pial.smth5 and lh.wm.smth5), I get the following error.
command: mris_place_surface --thickness lh.pial.smth5 lh.wm.smth5 20 5
lh.thickness
error: No such file or directory
error:
ERROR:
MRISreadVertexPositions(/Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/lh.wm.smth5):
surfaces differ. Main: 177753 verts 365096 faces, lh.wm.smth5: 145095
verts 298436 faces
Surfaces may be out-of-date
I understand there is a mismatch in the number of nodes of these
surfaces. How can I rectify this issue to get to the thickness?
Thanks and regards,
malav
Malav Shah
PhD candidate, Michael Brecht Lab,
Humboldt University zu Berlin.
(+49) 163-216-9391
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