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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:
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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 Main: 177753 verts 365096 faces, lh.wm.smth5: 145095 verts 298436 faces Surfaces may be out-of-date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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