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Thank you for a swift reply, Doug. Upon running the command "mris_diff --debug --min-dist lh.pial.5smth lh.wm.5smth 1 lh.thickness", the command line throws error that it can't find file. outcome:
5 --min-dist Use Exact = 1 Writing mindist to lh.thickness error: unknown file type for file (lh.thickness) mris_diff done
I tried with an absolute file path which also didn't work. Strangely, when mentioned no file location, but giving in a directory "mris_diff --debug --min-dist lh.pial.5smth lh.wm.5smth 1 /Users/user-name/Desktop/", 2 files namely COR-info and COR-001 are created on Desktop, and COR-info can be loaded as 'overlay' for a surface. Unfortunately, these curvature values are not within range at all.
For further details, using the command with --debug flag gives the following outcome (on command line)
Use Exact = 0 Writing mindist to /Users/monster/Desktop/ non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (177753, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure mris_diff done
Here I attach a couple of screenshots to elaborate the outcome. Kindly let me know how I can rectify the issue.
Thanks and regards, malav
From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 22, 2023 3:32:28 PM Subject: Re: [Freesurfer] Cortical thickness of elephant brain
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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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