Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Re: [Freesurfer] conversion of D-K atlas
by Fischl, Bruce R.,PHD 09 Jan '24

09 Jan '24

Hi Anna Parcellation is more than just format conversion - you need to map it onto the details of an individual subject's anatomy. In addition, the DKT atlas is only cortical. If you want subcortical regions in addition you should run recon-all as it will produce both. Cheers Bruce From: Arkhipova Anna, MUDr. <Anna.Arkhipova(a)fnol.cz> Sent: Tuesday, January 9, 2024 6:14 AM To: Freesurfer(a)nmr.mgh.harvard.edu; fischl <fischl(a)nmr.mgh.harvard.edu> Cc: phlustik(a)upol.cz Subject: conversion of D-K atlas External Email - Use Caution Dear prof. Fischl, We would like to kindly ask a question, if there is a way to convert Fressurfer Atlas Desikan-Killiany (lh and rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs) to Nifti file for parcellation of our resting-state fMRI data. Although we have tried script mri_convert, we obtained only cortical regions, but we need also subcortical regions. Would it be anyhow possible? Thank you so much in advance. Sincerely yours, Anna Arkhipova, MD fMRI laboratory Department of Neurology, Faculty of Medicine and Dentistry Palacky University and University hospital Olomouc Czech Republic

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SynthSR for T2-weighted images
by hmarzban＠student.ubc.ca 09 Jan '24

09 Jan '24

External Email - Use Caution Hello Eugenio, I wanted to inquire whether you have plans to create a tool for synthesizing T2-weighted low-field MRI images similar to SynthSR, which was developed for T1-weighted images. I'm in need of synthesizing T2-weighted images for Hyperfine, and I'm curious if there is a suitable method available for this purpose. Because, as I understand it, SynthSR transforms T2-weighted images into T1-weighted ones, and it is not designed for handling T2-weighted images. Is my understanding correct? Regards Hengameh

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Subject does not have a bstampfile
by Joanna Kidoń 09 Jan '24

09 Jan '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAw…, but I get the following error when I run the recon-all -all -s command: Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Sun Jan 7 20:48:46 CET 2024 ERROR: no run data found in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwu… Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NowakG exited with ERRORS at Sun Jan 7 20:48:46 CET 2024 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use. Best regards, Joanna -- ---------------------------------------------------------------------------------- dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w Katowicach PhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice

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dmri_pathstats error: segmentation fault after check the number of non-truncated streamlines
by Rosie 09 Jan '24

09 Jan '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to project my fiber tract endpoint into the inflated surface. According to the code in trac-paths, it needs to create the endpoint volume file by dmri_pathstats. But when the number of non-truncated streamlines is less than total streamlines, the program is terminated (but it works when the number is the same). my code: dmri_pathstats --intrk $tractpath --out right_stats --ends right_endpt --dtbase $fullpath$tensordata Then, I noted that dmri_projectEndPoints can do it straightly, but the usage make me confused. my code: dmri_projectEndPoints -i $tractpath -sl ./surf/lh.orig -sr ./surf/rh.orig -ol left_endpt.label -or right_endpt.label -ri ./T1_brain.nii.gz I wonder what should I do if I just want to project the fiber endpoint into the surface. FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.3.2 Platform: Ubuntu 18.04.5 on windows (WSL) Best, Rosie Zhou

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Re: [Freesurfer] Infant fs
by fsbuild 09 Jan '24

09 Jan '24

External Email - Use Caution  Sorry I cannot address those questions for you, but I have sent your email along to one of the developers. - R. On Jan 8, 2024, at 19:17, Amrita Pal <palamritaorama(a)gmail.com> wrote:        External Email - Use Caution        Thanks. I had filled out the form. How long do they take to respond? Also can I do subcortical thalamic segmentation with it? How is the LUT calculated both for infants and adults? Would you recommend an eleven year old's data analyzed by regular FS or infant FS?On Mon, Jan 8, 2024, 6:19 PM fsbuild <fsbuild(a)contbay.com> wrote: Looks like you need to fill out the request form,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/infantFS- R.On Jan 8, 2024, at 18:12, Amrita Pal <palamritaorama(a)gmail.com> wrote:        External Email - Use Caution        HelloI am trying to use the infant fs for processing my pediatric data. Where can I download the package?Thanks and Regards Amrita_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Infant fs
by Amrita Pal 08 Jan '24

08 Jan '24

External Email - Use Caution Hello I am trying to use the infant fs for processing my pediatric data. Where can I download the package? Thanks and Regards Amrita

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FS 6.0 outputs for use with 7.2 Tracula
by Alexopoulos, Dimitrios 07 Jan '24

07 Jan '24

External Email - Use Caution Can the tracula version in FS 7.x be used with surface outputs generated with FS 6.0? Our segmentations/surfaces generated with 6.0 look good but we'd like to generate the 42 WM pathways incorporated in FS 7x. Is this possible? I was under the impression the aparc+aseg segmentation is what is used by Tracula. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Tksurfer and freeview
by fsbuild 06 Jan '24

06 Jan '24

External Email - Use Caution  tksurfer has been deprecated and essentially replaced with tksurferfv bash shell script which runs freeview.   But whether or not you run the front-end tksurferfv bash script or the freeview command directly, I’m not aware of an option whereby you can tell freeview to run tcl/tk scripts.  My understanding is running tck/tk scripts as the -tcl switch allowed in tksurfer - is not supported in freeview. - R. - - - - -  $ tksurferfv --help This is a script that runs freeview with arguments like tksurfer. Not all tksurfer functionality is replicated. tksurferfv subject hemi surface .... -tksurfer : use tksurfer instead of freeview Can have multiple annotations -all : load white, pial, inflated -vgl : runs freeview with /usr/pubsw/bin/vglrun -no-vgl : does not run freeview with /usr/pubsw/bin/vglrun -no-outline : do not show annots as outline -neuro : use neurological orientation instead of radiological -rotate-around-cursor (-rca) : in 3d view, rotate around cursor (use -no- to turn off) -linear, -linearopaque, -piecewise, -min_to_max (default) : overlay heat scale tksurferfv dev On Jan 6, 2024, at 20:59, JAEHYUN KIM <jachos930@gmail..com> wrote:        External Email - Use Caution        Hello,I attempted to switch tksurfer to freeview in the script, but it seems like I need to change arguments "tcl" to something that can be applied to freeview.Option 'tcl' not recognized.What argument could possibly be used to replace tcl in the script such as tmp.tcl and lh pial -tcl??Best,Ed_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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    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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