Re: [Freesurfer] Cortical thickness of elephant brain

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

On 5/23/2023 1:12 PM, Malav Shah wrote:

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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

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*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

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*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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