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 Main: 177753 verts 365096 faces, lh.wm.smth5: 145095 verts 298436 faces Surfaces may be out-of-date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
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:
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 Main: 177753 verts 365096 faces, lh.wm.smth5: 145095 verts 298436 faces Surfaces may be out-of-date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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pjZSejN3qAoutdAz4ZgudZ-Fu9A0xaOD1oZyw-rIly2jzH...
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" 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
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
_______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] [ https://secure-web.cisco.com/1pjZSejN3qAoutdAz4ZgudZ-Fu9A0xaOD1oZyw-rIly2jzH... | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/15_r5s7HrLY1xgN7YJnocad__OsipsegEcn87FT8Hcd36lM... ]
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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
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" 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
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
_______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] [ https://secure-web.cisco.com/1pjZSejN3qAoutdAz4ZgudZ-Fu9A0xaOD1oZyw-rIly2jzH... | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/18N9laIfVpkzvIX1HeE67EfnwVfKfIN7-fJkeyQZwS8hrFx... ]
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/18N9laIfVpkzvIX1HeE67EfnwVfKfIN7-fJkeyQZwS8hrFx... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1VfuwLUQjoYUwUIkMSzpsaNyb1qwb9fzyLRrRwYQst48St_... https://secure-web.cisco.com/1VfuwLUQjoYUwUIkMSzpsaNyb1qwb9fzyLRrRwYQst48St_TPbWzaocyTubcmonPBaXRaqGrWercCuU-vObIixGV4TmBkV3aig8kp-AWKluiMtblVwgp4ay-kb6Ea8SRH2az8eCJluvtpnk1aGJ1v22IYZ6noFUsmSPV2RR72YiLQqmpQPyNoU_L-JaIj22-i03J8FkYWpVyz3Hlz_FY25Rb9zEIrGi2kLw2OpBMuY7spCM3yS_Lew0P2Bmcxg6DEtO5FFXH4Oo_wucVlG3hAO-wSw25AdZK_jdTobUOJsU4e82G_5FPBWlBKAFha2rGT/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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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" 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
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" 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
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1pHd2FhyANk6H5jYemlpaIIvNPlI8mHp2qbxb6VQjznEadNefvJLGzExZxXM4APUEJyA0wdzm2HfS_WN_9Sw-cpd5aPgUfc9_D_UtiVKDWM5_OmViVjuUWQkE2xXHDEITWiD2RkBKRaF5pKlS7liwVNV-I1ljXgO7hAFN-LeYHdZOtFK5wfoZ2sCwAtnEEZZ3a7TpoWMJXSw82vFw4fbu9HW9b41PeDQfQkISj0Uuqq84IQyTvSSvYTrwbClSLF3a/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1pjZSejN3qAoutdAz4ZgudZ-Fu9A0xaOD1oZyw-rIly2jzHFtOG9oN156MWYnTs-bef79cUtJym0G0xYLHZ0M5gshV7xrOIgi_03Md3YmlYwKACLVq5CDj9rMQZ4MCo1NTP3lR4V1-LEagN0k72Who-h0_u_QMnicijIghq9M_flwMMM0hxxgOZKtYFu5kETqpLaw_ahEzYBoGkKgeIcN4hFI8ZG_K3db_ptYxfRC-ciLyGbnI7yInxbcSvJ_Xs6h/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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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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Dear freeesurfer team, Thank you for your support. I have cortical thickness measurements. I want to know if I can visualise it on top of the pial matter surface. At the moment, I can see only white matter surface in its appropriate form. Pial surface looks more like a blanket on top of the grey matter, rather than bedsheet as it should ideally look. I understand that's the issue because Iextract pial matter with mri_tesselate command from tissue segmentation (white-, pial- and grey-matter labels). I think I am looking for pial matter surface that the command 'mris_place_surface' generates in traditional recon-all pipeline, and want to measure its curvature and surface area).
Can you please suggest how can use that command, or some other alternate to see pial mattter on top of the cortex?
Thank you in advance. - malav
From: "Malav Shah" malav.shah@bccn-berlin.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 25, 2023 4:32:55 PM Subject: Re: [Freesurfer] Cortical thickness of elephant brain
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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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Malav Shah