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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?
On 5/23/2023 1:12 PM, Malav Shah wrote:
External Email - Use Caution 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" [ mailto:malav.shah@bccn-berlin.de | malav.shah@bccn-berlin.de ] To: "Freesurfer support list" [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] Sent: Monday, May 22, 2023 5:35:56 PM Subject: Re: [Freesurfer] Cortical thickness of elephant brain
External Email - Use Caution 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" [ mailto:dgreve@MGH.HARVARD.EDU | dgreve@MGH.HARVARD.EDU ] To: "freesurfer" [ mailto:freesurfer@nmr.mgh.harvard.edu | 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
On 5/22/2023 5:48 AM, Malav Shah wrote:
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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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