Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
by fsbuild 06 Jan '24

06 Jan '24

External Email - Use Caution    Your Linux image could be missing system files and/or graphics card driver updates needed for the version of Qt included with Freeview to display graphics via X-Windows.  So I would first remove whatever currently exists under /usr/local/freesurfer and then follow the instructions on the Wiki page to do an install from scratch using the actual installer (instead of the tar file).  The instructions are here, https://secure-web.cisco.com/1aVasdKo9Pwif5UQ2Uch0IDTvauLowJGIckrOUQbXQ2Ugj… After you install Freesurfer and setup the X-server on the Windows host - stop and verify basic graphics are working by running glxgears.  If communication from Linux running under WSL is working with the X-server on the Windows host, then you will see an X-Window open and display the spinning gears via the following Linux commands, $ sudo apt-get install mesa-utils .... answer Y to all prompts ... output deleted ... $ which glxgears /bin/glxgears $ glxgears The instructions on the wiki page end with running the "freeview" command with no arguments in order to test freeview can at least open and display an empty window. If that works try displaying one of the volume files included in freesurfer, $ freeview  $FREESURFER_HOME/subjects/bert/mri/brain.mgz If that works, then try displaying one of your surfaces/volumes with your own freeview command. If however glxgears worked, but the freeview command failed to open a window and/or display the volume as listed above, then the next step is to check for an upgrade to the OpenGL drivers on your Windows host.  Freeview needs newer revisions of OpenGL in order to display graphics.  Once you update the drivers, try running the freeview commands listed above again. BTW - please remember to change SUBJECTS_DIR from $FREESURFER_HOME/subjects in your shell environment to a path your normal userid can write to w/o sudo/admin privs.  That could be in your home directory e.g., $ cd $ mkdir subjects $ export SUBJECTS_DIR=$HOME/subjects You could put that export command in your shell init, e.g., $HOME/.bashrc file - R. On 1/6/24 13:25, Flemister, Abeoseh B. (flemistera(a)missouri.edu) wrote: I’m using Ubuntu.  Abeoseh Flemister From: Flemister, Abeoseh B. <flemistera(a)missouri.edu> Sent: Saturday, January 6, 2024 12:24:40 PM To: fsbuild <fsbuild(a)contbay.com>; freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS   No, I installed using tar.gz freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz Abeoseh Flemister From: fsbuild <fsbuild(a)contbay.com> Sent: Friday, January 5, 2024 9:35 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Flemister, Abeoseh B. <flemistera(a)missouri.edu> Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS     Did you install Freesurfer 7.4.1 using the Debian installer package ? https://secure-web.cisco.com/1IOiqTlEkTSd5OYr_A3naRtVr5L_K5zRpteC0_uUt7M0gR… - R. On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemistera(a)missouri.edu> wrote:         External Email - Use Caution         Thanks, but the issue isn't that graphics aren't displaying, it's that freeview won't load because qt can't be initialized.  Abeoseh Flemister From: fsbuild <fsbuild(a)contbay.com> Sent: Friday, January 5, 2024 8:27 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Flemister, Abeoseh B. <flemistera(a)missouri.edu> Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS     For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "Re: [Freesurfer] Freeview not showing output",  https://secure-web.cisco.com/1KBH0OQxJdEKdxK38EEhCdBUjp55VUN1FBiZ5YthIc5pA6… In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL above, that link is, https://secure-web.cisco.com/13SNvKLnlnBhGoPqHE-K7O3s6HLiLweiBx06mragNvW-EW… - R. On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. <flemistera(a)missouri.edu> wrote:         External Email - Use Caution         Hi Yujing, Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve unfortunately run into another error: This application failed to start because no Qt platform plugin could be initialized. I saw an email on this topic but I don't think it was ever answered.. Apologies if I'm reading the thread wrong. Any help would be greatly appreciated! Abeoseh Flemister From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Sent: Friday, January 5, 2024 3:05 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS   WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. This is from your recon-all.log “ mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz   mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz") “   There is a space in your path to nii.gz.. Can you remove the space by renaming the directory?   Also, your SUBJECTS_DIR points to your Freesurfer install directory - /usr/local/freesurfer/subjects. You might run into permission or symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions.   Best,   Yujing   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B. Sent: Friday, January 5, 2024 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS           External Email - Use Caution         Hi FreeSurfer Team,   I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains.    I attached my recon-all.logs.. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions!   Thanks, Abeoseh Flemister _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dKi8DOAV1nss_Bnp3qOnf-h1VRr85LxYAYyImsYicVwlX… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1dKi8DOAV1nss_Bnp3qOnf-h1VRr85LxYAYyImsYicVwlX…

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Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
by fsbuild 06 Jan '24

06 Jan '24

External Email - Use Caution  Did you install Freesurfer 7.4.1 using the Debian installer package ?https://secure-web.cisco.com/1Q45DaXEMcahL0g3wyejOntK1tGwx5UNQU25fdIi6ImofQsUOBUFGOhQ21vBk8sDRQfWWELU7ghl6F8QsJA6G2LpBun8SBG8VuebFtJaMobqrOERog6kz0hiKLV9ajDE2AKC1cpczWaDYkcSc4gMj3M6RFSGVTMvswdtfRVwJb-Ck23miRyGdEEMqm_Vf-b-J9o0O3vxunBYSB4cBN28DNJm4do5FWUZ4zSzRajltNg7RZ46COiMaso4uOBO2RYGe0GsZu0-WtJ9Aceq0QL43ZSK1SlxBsNnkMA4gJsKlawl_Tl3esT3lDUmN4303CUV1bHuzWMUv-G-vhN66uSWjhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb- R. On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemistera(a)missouri.edu> wrote:        External Email - Use Caution        Thanks, but the issue isn't that graphics aren't displaying, it's that freeview won't load because qt can't be initialized. Abeoseh FlemisterFrom: fsbuild <fsbuild@contbay.com>Sent: Friday, January 5, 2024 8:27 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Flemister, Abeoseh B. <flemistera@missouri.edu>Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS  For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "Re: [Freesurfer] Freeview not showing output", https://secure-web.cisco.com/1oaJ0JSPhxlRjzZbZiQ7yaftYm3TvYL5vsUqSvRIwn1mxTLB9TJXbethBhfapiwejmtZvkPk-Rzn2z_ad008-CzQlNve-NK6CceUt0VtPPFJdwtHKP55BXcuQhcU1YMz4-FPp9GzSTpiJ3JHu0iWTdbP786ULqlSTxSVgPgP7VkSxFmOR08R6XsMAhtGAScfuIli7yeGgO6_pGTXQjtPhYf_rpwzgCC2fxaK-4G43kajshNd4Ud6bVNH54fIM-6dcft-18wReIbRAerhMZzSx7hql2Jiwn18OCmUKqAcP8rn9FrqtaYOtu1LGeBs5QWaxiqN9ZGDiVySHjpAlv-EeZg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.htmlIn case the link to the Freesurfer WIKI talking about WSL is garbled in the URL above, that link is,https://secure-web.cisco.com/1EiWtVy6tBY8avsFO7RwETRF3_M-X-xF2Kpa7qQsUO9… R.On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. <flemistera(a)missouri.edu> wrote:        External Email - Use Caution        Hi Yujing,Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve unfortunately run into another error: This application failed to start because no Qt platform plugin could be initialized.I saw an email on this topic but I don't think it was ever answered.. Apologies if I'm reading the thread wrong. Any help would be greatly appreciated!Abeoseh FlemisterFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>Sent: Friday, January 5, 2024 3:05 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System.. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.This is from your recon-all.log“mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“ There is a space in your path to nii.gz. Can you remove the space by renaming the directory? Also, your SUBJECTS_DIR points to your Freesurfer install directory - /usr/local/freesurfer/subjects. You might run into permission or symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions. Best, Yujing From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B.Sent: Friday, January 5, 2024 3:31 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS         External Email - Use Caution        Hi FreeSurfer Team, I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains.  I attached my recon-all.logs.. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions! Thanks,Abeoseh Flemister_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_error_no_clear_message
by fsbuild 06 Jan '24

06 Jan '24

External Email - Use Caution If you do a case insensitive search for the string “error" in the log, you should see there are multiple listings of,  IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES out of QuasiNewtonEMA: 008: -log(p) =   -0..0  tol 0.000010 This thread indicates it could be the skull stripping is not right, and should be checked,https://secure-web.cisco.com/1diiACwYbRU5h086AYSNGiqllYdOKITn3ySdC0… R. On Jan 6, 2024, at 01:10, yunus soleymani <soleymani.yunus(a)yahoo.com> wrote:        External Email - Use Caution        Hi Fargol,I recently heard about some problems from my coworkers who were using Ubuntu 18 and version 7.2.0 of the software. However, I am currently using version 7.2.0 on Ubuntu 22.04.2 LTS, and it works well for me. You could try it out and see if it works for you as well.bests,Yunus--------------------------------------------------------------------------------Yunus SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------On Friday, January 5, 2024 at 10:05:54 PM GMT+3:30, Fargol Rezayaraghi <fargor(a)uw.edu> wrote:        External Email - Use Caution        Hi FreeSurfer Team,I hope this email finds you well. I'm trying to use a T1 image to get the aparc+aseg and wmparc nifti files. I was using this command:  recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s Subject1 -i T1.nii - all first, and after getting Talairach error, I added -nota -check at the end).I'm getting the following messages without a clear error number: recon-all -s Subject1 exited with ERRORS at Thu Dec 14 21:18:02 EST 2023For more details, see the log file /home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.logTo report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1n6sdsWRV3TG8Jv2QrC7lr2OJkNo-vKWiVDfRMi… version of the freesurfer: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bMy platform is ubuntu 18_04_06 on Oracle VM VirtualBoxI've attached the log file. -- Kind Regards,Fargol R. Araghi (Rezayaraghi)Ph.D. Candidate, University of WashingtonDepartment of Mechanical EngineeringMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1MEbXNSnnv7NT1-4EzMYIfzctR98Iydj5J9JFwf… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WLCgxPTXYmh2RXigsOXigGsIv-l-w5--kmcWP… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_error_no_clear_message
by Fargol Rezayaraghi 06 Jan '24

06 Jan '24

External Email - Use Caution Hi FreeSurfer Team, I hope this email finds you well. I'm trying to use a T1 image to get the aparc+aseg and wmparc nifti files. I was using this command: recon-all -s Subject1 -i T1.nii - all -notal -check ( I used recon-all -s Subject1 -i T1.nii - all first, and after getting Talairach error, I added -nota -check at the end). I'm getting the following messages without a clear error number: recon-all -s Subject1 exited with ERRORS at Thu Dec 14 21:18:02 EST 2023 For more details, see the log file /home/developer/Desktop/freesurfer/7.2.0/subjects/Subject1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1BSxCZVaZV339Q-WAflS64QucA-5MEBgQ3fZ93nAe5XWzCQ… The version of the freesurfer: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b My platform is ubuntu 18_04_06 on Oracle VM VirtualBox I've attached the log file. -- Kind Regards, *Fargol R. Araghi (Rezayaraghi)* Ph.D. Candidate, University of Washington Department of Mechanical Engineering http://secure-web.cisco.com/1mfGgLjPrxUPgiKW0cYrI4VYHOlB7NRl1ofAIWpOAZsNxTO… <https://secure-web.cisco.com/1Qo3Un4JrwSuFjRmc8vXXpxZPVUMbj7_Qo9FxT9GOWDuUQ…>

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Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
by fsbuild 05 Jan '24

05 Jan '24

External Email - Use Caution  For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "Re: [Freesurfer] Freeview not showing output",  https://secure-web.cisco.com/1_xzs3l0H18glGmrIaq7DLLWEnbalu4hRqRVJfIOVshijK… In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL above, that link is, https://secure-web.cisco.com/1NIeWPFmWL9ULg_YLAREetdCKnwA4CAjtUSmmia-2fJLau… - R. On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. <flemistera(a)missouri.edu> wrote:        External Email - Use Caution        Hi Yujing,Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve unfortunately run into another error: This application failed to start because no Qt platform plugin could be initialized.I saw an email on this topic but I don't think it was ever answered. Apologies if I'm reading the thread wrong. Any help would be greatly appreciated!Abeoseh FlemisterFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>Sent: Friday, January 5, 2024 3:05 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.This is from your recon-all.log“mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“ There is a space in your path to nii.gz. Can you remove the space by renaming the directory? Also, your SUBJECTS_DIR points to your Freesurfer install directory - /usr/local/freesurfer/subjects. You might run into permission or symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions. Best, Yujing From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B.Sent: Friday, January 5, 2024 3:31 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS         External Email - Use Caution        Hi FreeSurfer Team, I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains.  I attached my recon-all..logs. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions! Thanks,Abeoseh Flemister_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all -s SiroSTC006_pre exited with ERRORS
by Flemister, Abeoseh B. 05 Jan '24

05 Jan '24

External Email - Use Caution Hi FreeSurfer Team, I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread <https://secure-web.cisco.com/1dNYuQ5feZYQ6hNc76goinSvD-Ypnc3onN5YQA8IZaGD9Z…> where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains. I attached my recon-all.logs. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions! Thanks, Abeoseh Flemister

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WMH-SynthSeg vs. SAMSEG for WM lesions
by Stefano Cerri 05 Jan '24

05 Jan '24

External Email - Use Caution Hi, For SAMSEG: Are you using the --lesion-mask-pattern flag with the value "1" on the FLAIR scan? You can try to relax the masking by excluding darker than WM mean intensities voxels rather than darker than GM ones, i.e., by adding to your command: --lesion-mask-structure "White" For WMH-SynthSeg: It looks like a memory error (the process was killed). On the Wiki: https://secure-web.cisco.com/1HuCfTaru0pjBRImg5FBdnCDAClGBp2QhQDG_ONxySiD4a… they recommend 32GB of RAM. Do you have access to a machine with more RAM? Stefano [Freesurfer] WMH-SynthSeg vs. SAMSEG for WM lesions <https://secure-web.cisco.com/10UF5Sfsck6gBiuQyh4tRFtvmnzLpFEUi-WgbbCbj9UG2b…> SudEEpti <https://secure-web.cisco.com/1oJN1ySIU6hTF6KozyWDOxPUxnfQT6NbHWVuqvL4RV_PNw…> Thu, 04 Jan 2024 23:54:04 -0800 <https://secure-web.cisco.com/1JsH5pJG8BzMI3v8LKsEGcmt1J0aRmNdo-KqIrQw8arF8B…> External Email - Use Caution Hello Freesurfer I am reaching out for some advice on unsupervised WM lesion detection using SAMSEG and WMH-SynthSeg. *SAMSEG: * Our use case prioritizes maximizing true positives over minimizing false positives. However, even with a low threshold of 0.1, SAMSEG misses some areas (on FLAIR). Are there any strategies or parameters to force SAMSEG to be more "aggressive"? *WMH-SynthSeg:* Unfortunately, I have not been able to get WMH-SynthSeg to work. The error message is pasted below. Does this point to a memory issue (I have 24GB RAM)? *Arguments seem correct; loading Python packages...Using cpuUsing 1 thread(s)Preparing model and loading weightsWorking on image 1 of 1: /home/localuser01/southekal/TEMP/101-001_3scans_FLAIR/101-001-1_reg.mgz Loading input volume and normalizing to [0,1] Upscaling to target resolution Pushing data through the CNNKilledreal 3m33.897suser 2m48.028ssys 0m32.337s* Any insights or suggestions would be greatly appreciated! Thank you in advance. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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problem with using freeview to load flattened patches
by Nasr, Shahin,Ph.D. 05 Jan '24

05 Jan '24

Dear Surfers, I am using freesurfer 7.1.1 to view flattened patches and I have faced two issues: 1) When I elevate the camera (see the command below), the loaded image is not centered. Is there any command (key) to recenter the image other than manually moving it? 2) The "measure" bottom is not active and I can't find any way to show the 1 cm scale bar. This is the command line that I am using to load the image: freeview -f <Subject Folder>/surf/rh.inflated:patch=rh.occip_patch.flat:curvature=<Subject Folder>/surf/rh.curv.subdiv.B1justsub.mgh:edgethickness=0:annot_outline=1:overlay=<FMRI Data>/sig.nii.gz:overlay_threshold=2,4 -viewport 3d -zoom 1.2 -cam Elevation 90 Regards, Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://mesovision.martinos.org/

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WMH-SynthSeg vs. SAMSEG for WM lesions
by SudEEpti 05 Jan '24

05 Jan '24

External Email - Use Caution Hello Freesurfer I am reaching out for some advice on unsupervised WM lesion detection using SAMSEG and WMH-SynthSeg. *SAMSEG: * Our use case prioritizes maximizing true positives over minimizing false positives. However, even with a low threshold of 0.1, SAMSEG misses some areas (on FLAIR). Are there any strategies or parameters to force SAMSEG to be more "aggressive"? *WMH-SynthSeg:* Unfortunately, I have not been able to get WMH-SynthSeg to work. The error message is pasted below. Does this point to a memory issue (I have 24GB RAM)? *Arguments seem correct; loading Python packages...Using cpuUsing 1 thread(s)Preparing model and loading weightsWorking on image 1 of 1: /home/localuser01/southekal/TEMP/101-001_3scans_FLAIR/101-001-1_reg.mgz Loading input volume and normalizing to [0,1] Upscaling to target resolution Pushing data through the CNNKilledreal 3m33.897suser 2m48.028ssys 0m32.337s* Any insights or suggestions would be greatly appreciated! Thank you in advance.

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Re: [Freesurfer] Freeview not showing output
by fsbuild 04 Jan '24

04 Jan '24

External Email - Use Caution As Ruopeng said, even if simple X-Windows programs like glxgears run, that does not mean freeview will display graphics. If freeview is not displaying images after X-ming (or a different)  X-Windows server runs on the Windows host and displays graphics from glxgears, then there is likely something not right with the OpenGL drivers working with the graphics hardware on the Windows host.  Usually the fix is to update to the latest OpenGL drivers on the Windows host. If you have not read through or tried the steps on this Wiki page, then it might help,   https://secure-web.cisco.com/12p37USRW5-RyLF2YXnbTAoizwyX5lHFSny043woIbJwaV… If you are seeing graphics from glxgears then I would presume DISPLAY and XDG_RUNTIME_DIR are likely set OK in Linux. - R. On Jan 4, 2024, at 10:08, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:It appears your system has some problem displaying OpenGL content properly. I’m not familiar with Xming. Can you try some other x display for Windows such as mobaxterm?https://secure-web.cisco.com/1KYKTifNL0XRk6k_SapoZX6CTHF_pDgzD6UK… Jan 4, 2024, at 6:11 AM, Shawa, Zeena <zeena.shawa.20(a)ucl.ac.uk> wrote:        External Email - Use Caution        Hi Ruopeng, Thank you for your quick reply!When running glxgears I just see a blank window. Sincerely,Zeena Shawa From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wang, RuopengSent: Wednesday, January 3, 2024 4:29 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Freeview not showing output ⚠ Caution: External sender What if you run glxgears command? Do you see 3D spinning gears or just a blank window? RuopengFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shawa, Zeena <zeena.shawa.20@ucl.ac.uk>Sent: Wednesday, January 3, 2024 9:17:00 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Freeview not showing output         External Email - Use Caution        Hello FreeSurfer Developers and Community, Hope your day has been going well and happy new year! I'm attempting to visualise FreeSurfer outputs using freeview, as described on the “Introduction to Freesurfer Output” tutorial, under the “Viewing Volumes with Freeview” section (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1wzX4cge9MlMx5r_8jnAVeO8ue9DOKEESG6wS-…;) The viewer launches fine and seems to load everything, but instead of showing any output it simply shows a black screen in the middle (screenshot attached). There is no error outputted in the command line either. The viewer seems to work fine otherwise, and I have completed the Xming X-server setup as described here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/18qHMAU0T79b7NwnKw9Zpf5tUXLvkF9EnPH2_5…'ve searched the archives and GitHub issues and cannot find a similar error. I would appreciate any feedback on how to troubleshoot this issue.Thank you very much for your understanding and help!  FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460Freeview version: Version 3.0, June 14 2023 buildXming versions: Xming fonts 7.7.0.10, Xming 6.9.0.31Platform: WSL2 Ubuntu 22.04.3 LTSuname -a: Linux LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxspecific command: freeview -v \good_output/mri/T1.mgz \good_output/mri/wm.mgz \good_output/mri/brainmask.mgz \good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \-f good_output/surf/lh.white:edgecolor=blue \good_output/surf/lh.pial:edgecolor=red \good_output/surf/rh.white:edgecolor=blue \good_output/surf/rh.pial:edgecolor=red  Sincerely,Zeena Shawa Zeena Shawai4Health PhD StudentAlan Turing Institute – Roche Community ScholarResearch Group UCL Centre for Medical Image Computing  <image001.png><image002.png> _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer January 2024