Dear Douglas,

using .mgz worked well.

As the command is supposed to generate a "curvature" file, I assumed it to be a surface format.

Thanks a bunch.

with regards,

Malav

From: "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, May 24, 2023 3:46:35 PM
Subject: Re: [Freesurfer] Cortical thickness of elephant brain

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Can you try using lh.thickness.mgz instead of just lh.thickness?

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Hi there,

I believe the problem occured, because I generated pial surface by segmenting, and then tessellating that label volume, instead the way I see in log file of the subject 'bert' where standard autorecon achieves it using the 'mris_place_surface' command

(mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 8 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white)

Therefore, to go that way, I tried to "cheat" freesurfer with

"mris_place_surface --adgws-in autodet.gw.stats.lh.dat --invol vol_seg.nii.gz --lh --i lh.wm.5smth --o lh.pial.nofix --pial --repulse-surf lh.wm.5smth"

command using (following) made-up files....

- vol_seg.nii.gz- segmentation volume with voxel-intensities 1 (pial-matter), 2 (gray matter) and 3 (white matter)

- lh.wm.smth- white matter surface generated using white matter segmentation's tessellation, and then smootheed with n_smooth = 5

- autodet.gw.stats.lh.pial is duplicated from the subject "bert" file with following values

hemicode           1
white_border_hi    3
white_border_low   3
white_outside_low  3
white_inside_hi    3
white_outside_hi   3
pial_border_hi    1
pial_border_low   1
pial_outside_low  1
pial_inside_hi    1
pial_outside_hi   1
use_mode 1
variablesigma 1.000000
std_scale 1.000000
adWHITE_MATTER_MEAN 3
MAX_WHITE 3.00000
MIN_BORDER_WHITE 2.500000
MAX_BORDER_WHITE 2.5000000
MAX_GRAY 2.000000
MID_GRAY 2.000000
MIN_GRAY_AT_CSF_BORDER 1.5000000
MAX_GRAY_AT_CSF_BORDER 1.5000000
MIN_CSF 0.000000
adMAX_CSF 1.0000000
white_mean 3.000000
white_mode 3.000000
white_std 0
gray_mean 2.000000
gray_mode 2.000000
gray_std 0
min_border_white 2.000000
max_border_white 3.0
min_gray_at_white_border 1.5
max_gray 2.00
min_gray_at_csf_border 1.500
max_gray_at_csf_border 2.44
min_csf 1.000000
max_csf 1.000000
max_gray_scale 0.000000
max_scale_down 0.200000

However...I am getting the segmenetation fault error when it reads the surface

cd /Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/fs_trl2
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects/
mris_place_surface --adgws-in autodet.gw.stats.lh.dat --invol vol_seg.nii.gz --lh --i lh.wm.5smth --o lh.pial.nofix --pial --repulse-surf lh.wm.5smth

Reading in input surface lh.wm.5smth
ERROR: MRISedges(): too many faces: 181 938 n=7, m=3, k=2
Segmentation fault: 11

Any suggestions?

Thanks in advance,

malav

---

From: "Malav Shah" <malav.shah@bccn-berlin.de>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, May 22, 2023 5:35:56 PM
Subject: Re: [Freesurfer] Cortical thickness of elephant brain

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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:

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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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