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

        External Email - Use Caution        

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

        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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