Freesurfer September 2024

freesurfer@nmr.mgh.harvard.edu

48 participants
58 discussions

Freesurfer - skull stripping error
by De Giorgi, Sara 29 Sep '24

29 Sep '24

Dear all, Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks: [cid:22ca1ab1-56b5-42b4-a482-23e883ecfab5] This is how the skull stripping appears: [cid:b3faf493-9947-4d50-a296-1f0456d5382d] Please find the log file as an attachment. I also tried to manually adjust brainmask.mgz , but also brain.mgz is incorrect. How can I solve this issue? Thanks, Sara

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Qt platform and lta_convert error
by Mohammad Amin Khodadadegan 28 Sep '24

28 Sep '24

External Email - Use Caution when I ran freeview ,I have encounter with this error: freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Aborted (core dumped) when I run the reconstruction command,I encounter with this error: fs-check-version --s subj04 --o /tmp/tmp.oDwgAc Sat Sep 28 20:00:24 +0330 2024 setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjects cd /home/ubuntu freesurfer/bin/fs-check-version --s subj04 --o /tmp/tmp.oDwgAc -rwxrwxr-x 1 1623927 1623927 18565 Jun 14 2023 freesurfer/bin/fs-check-version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 $Id$ Linux freesurferubuntu 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux pid 6375 Current FS Version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/ubuntu/freesurfer/subjects Actual FREESURFER_HOME /home/ubuntu/freesurfer Linux freesurferubuntu 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux lta_convert: Command not found. ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?'

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dev builds available for rocky Linux and silicon MacOS (M1, M2, M3 processors)
by fsbuild 27 Sep '24

27 Sep '24

External Email - Use Caution  In response to requests for freesurfer on Rocky8, Rocky9 linux and silicon macs (with M1, M2, M3 processors), there are updated, relatively stable development builds, i.e., builds that have gone thru some testing, available from https://secure-web.cisco.com/1GcRpXukAZA_u5fux2mIvH7rGNj6Iwz7089dTqiW5XwIhC… For Rocky8 or Rocky9 Linux, it should work to install the rpm, freesurfer-Rocky8-7.0.0-dev.x86_64.rpm For MacOS on Apple silicon machines with an M1, M2, M3 processor, you can try the .pkg installer, freesurfer-macOS-darwin_arm64-dev.pkg.  This has been tested on MacOS Monterey, Ventura and Sonoma, BUT NOT Sequoia which was just released. Please let us know if you run into issues. - R.

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trac-all longitudinal error
by Nelson, Eric (Campus) 23 Sep '24

23 Sep '24

External Email - Use Caution Hello all, I am trying to run trac-all prep longitudinally (testing it on a single subject for now with three timepoints and 2 scans per time point). I keep getting the below error. Can't figure out what is causing it and could use some advice. I've also attached the trac-all.log from my base file and the configuration file (configfile.test). Any help would be greatly appreciated Checking inputs error: niiRead(): error opening file /data/project/lahtilab/eanelson/FreeSurfer_7.1.1/Prisma_Data/OUTPUT/Freesurfer/Long/sessions_1-3/sub-control04_ses-01.long.sub-control04_base/dlabel/anatorig/aparc+aseg_mask.nii.gz ERROR: reading /data/project/lahtilab/eanelson/FreeSurfer_7.1.1/Prisma_Data/OUTPUT/Freesurfer/Long/sessions_1-3/sub-control04_ses-01.long.sub-control04_base/dlabel/anatorig/aparc+aseg_mask.nii.gz Linux c0231 3.10.0-1160.24.1.el7.x86_64 #1 SMP Thu Mar 25 21:21:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Sep 17 13:48:41 CDT 2024 Best, Eric

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Questions re Freesurfer editing
by Bronwyn Overs 22 Sep '24

22 Sep '24

External Email - Use Caution Dear Mailing List, Can you please tell me how to address the following issues in Freesurfer version 5.3? 1. Medial surface issues where the LH and RH Pial surfaces overlap (indicated by orange circles in the attached 'medial_surface_issue.jpg'). Is this an issue that needs to be address, and if so, how is it done? 2. Regions of non-brain that have been labelled as cerebellum in the aseg file (indicated by the red circles in the attached image 'cerebellum_inclusions.jpg'). Can I rerun the skull stripping step or simply delete the erroneous voxels form the volume? Kind regards, Bronwyn Overs Senior Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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fresurfer on silicon macs (was Re: Trying to run freeview via Docker/XQuartz and it just aborts
by fsbuild 20 Sep '24

20 Sep '24

External Email - Use Caution  Try downloading and installing the development build for the silicon Mac from,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-… don’t really support running/debugging X-Windows applications like freeview thru docker back to the host.  For the case where freeview does not run natively, many people choose a VM image with its own built in X-server, e.g., run VirtualBox on Windows. There are however ubuntu debian package installers located in the same directory as the mac package listed above, i,.e., there is an Ubuntu 22 .deb installer.  If you don't use the linux install tools to install the .deb package, then you will likely be missing system libraries. - R. On Sep 20, 2024, at 14:36, Belakovski, Nickolai <nickolai.belakovski(a)mssm.edu> wrote:        External Email - Use Caution        Hello all, I'm just getting started with Freesurfer so please forgive me if I'm missing something basic, but basically my setup is like this: I'm on an M3 Mac and I'd like to run FreeSurfer. Since there's arm/x86 compatibility issues I'm trying to run it inside of an x86_64 docker image of Ubuntu 22.04. I've downloaded the relevant .tar.gz, mounted it inside my docker and I've installed all the various packages I need to run freeview (basically I tried to run freeview and every time it complained about a shared lib not found I'd install the relevant package), but now I've gotten to a point where I try to run freeview and it just says "Aborted" and that's it. I have a license.txt at FREESURFER_HOME and I've run source SetUpFreeSurfer.sh, but basically I'm stuck at this point. I can run freeview -h and get the help message. I can run freeview --verbose, but this also just results in an "Aborted" message and that's it. Is there anything else I can do to debug? The "Aborted" message unfortunately doesn't give me much to go on 🙁 For the sake of completeness I'll just make a note that I should be able to run this through Docker. I've installed x11-apps and run xeyes in the same container in which I'm trying to run freeview and it works, so I don't think that's the part it's choking on. Also for completeness here's a list of the packages I had to apt-get install: libgomp1, libgl1, libglib2.0-0, libqt5gui5, and I also had to export LIBGL_ALWAYS_INDIRECT=1 for some reason. Thanks very much for your help,Nickolai BelakovskiBiomedical Software EngineerBioMedical Engineering and Imaging Institute (BMEII)Icahn School of Medicine at Mount Sinai _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Trying to run freeview via Docker/XQuartz and it just aborts
by Belakovski, Nickolai 20 Sep '24

20 Sep '24

External Email - Use Caution Hello all, I'm just getting started with Freesurfer so please forgive me if I'm missing something basic, but basically my setup is like this: I'm on an M3 Mac and I'd like to run FreeSurfer. Since there's arm/x86 compatibility issues I'm trying to run it inside of an x86_64 docker image of Ubuntu 22.04. I've downloaded the relevant .tar.gz, mounted it inside my docker and I've installed all the various packages I need to run freeview (basically I tried to run freeview and every time it complained about a shared lib not found I'd install the relevant package), but now I've gotten to a point where I try to run freeview and it just says "Aborted" and that's it. I have a license.txt at FREESURFER_HOME and I've run source SetUpFreeSurfer.sh, but basically I'm stuck at this point. I can run freeview -h and get the help message. I can run freeview --verbose, but this also just results in an "Aborted" message and that's it. Is there anything else I can do to debug? The "Aborted" message unfortunately doesn't give me much to go on 🙁 For the sake of completeness I'll just make a note that I should be able to run this through Docker. I've installed x11-apps and run xeyes in the same container in which I'm trying to run freeview and it works, so I don't think that's the part it's choking on. Also for completeness here's a list of the packages I had to apt-get install: libgomp1, libgl1, libglib2.0-0, libqt5gui5, and I also had to export LIBGL_ALWAYS_INDIRECT=1 for some reason. Thanks very much for your help, Nickolai Belakovski Biomedical Software Engineer BioMedical Engineering and Imaging Institute (BMEII) Icahn School of Medicine at Mount Sinai

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Hippocampal segmentation on two sets of MRI with different resolution
by Jacob Bunyamin 20 Sep '24

20 Sep '24

External Email - Use Caution Good afternoon, I have two sets of MRIs with different resolutions (0.9mm3 and 1mm3 isotropic). At the moment I ran the hippocampal segmentation on both so I assume that the volume I obtained from 0.9mm3 was downsampled to 1mm3 after recon-all. I just read that recon-all allows us to keep the resolution using the -cm flag, the question is would the volume I obtain after rerun with -cm from 0.9mm3 scans be comparable with the volume I obtained from the other set (the 1 mm3 scans) or is it better to keep the downsampled ones? Some subjects also have high-resolution T2 (0.4x0.4x2 mm3) scans, would running the recon-all with -cm affect the T1+T2 segmentation result as well? Thank you very much. Kind regards, Jacob -- *Jacob Bunyamin* PhD Student *Department of Neuroscience* School of Translational Medicine Monash University *E:* jacob.bunyamin(a)monash.edu

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Transforming aseg.mgz to native anatomical space - transform files absent
by Christine Farrugia 20 Sep '24

20 Sep '24

External Email - Use Caution Hi, I'm trying to convert the aseg output of my longitudinal runs from FreeSurfer space back to native anatomical space by following the directions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat However, I've noted that none of my subjects have a <tpid>_to_<tpid>.long.<baseid>.lta transformation in <tpid>.long.<baseid>/mri/transforms. The transformations from each of the longs to the base (and vice-versa) are in the mri/transforms folder of the <templateid> directory, but that's about it, despite the fact that recon-all finished without errors. I'm using FreeSurfer v7.4.1. Is this a feature of FreeSurfer v7 or is something going wrong somewhere? Thanks in advance, Christine The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Re: [Freesurfer] Running Freeview from Ubuntu (on WSL)
by fsbuild 19 Sep '24

19 Sep '24

External Email - Use Caution   It would be good to know what version of Ubuntu you are running in WSL.   You can see that in the Ubuntu linux terminal window with the command below, and you should see something like the following ... $ cat /etc/os-release PRETTY_NAME="Ubuntu 22.04.5 LTS" NAME="Ubuntu" VERSION_ID="22.04" VERSION="22.04.5 LTS (Jammy Jellyfish)" VERSION_CODENAME=jammy ID=ubuntu ID_LIKE=debian HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" UBUNTU_CODENAME=jammy - which in this case indicates Ubuntu 22. I would also check you used the Ubuntu 22 .dev installer package from, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubu… - and installed it from wherever you downloaded it to on the Ubuntu system with the command, $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb If you didn't use that installer, then the system may be missing xcb related files it needs to run Qt, etc. If you got that Qt error even after the freesurfer .deb package install completed with no errors, then you could try the commands, $ xhost +local: $ sudo apt-get install --reinstall libxcb-xinerama0 Please note you need a license.txt file for freeview to find.  You can put that in your $HOME directory on linux and set the environment variable FS_LICENSE to point to it $ export FS_LICENSE=$HOME/license.txt $ head -1 $FS_LICENSE you(a)somewhere.com    <-----  email address you used to reigster via the form, Then try running freeview again (with no arguments to see if it can open an empty window).  $ freeview - R. On 9/19/24 17:31, Barsotti, Ercole (john-barsotti(a)uiowa.edu) wrote:         External Email - Use Caution         Just re-upping this message in case anyone has any ideas. :) Hi all, I've successfully downloaded Freesurfer version 7.4 and can run its commands, with the exception of Freeview. I downloaded and installed Xming, like the FreeSurfer instructions tell you (https://freesurfer.net/fswiki/FS7_wsl_ubuntu) but this does not seem to work, either. I am using Ubuntu on a Windows computer. I get the following error when I run the freeview command : This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted Best, John From: Barsotti, Ercole <john-barsotti(a)uiowa.edu> Sent: Thursday, September 19, 2024 12:21 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Running Freeview from Ubuntu   Hi all, I've successfully downloaded Freesurfer version 7.4 and can run its commands, with the exception of Freeview. I downloaded and installed Xming, like the FreeSurfer instructions tell you (https://freesurfer.net/fswiki/FS7_wsl_ubuntu) but this does not seem to work, either. I am using Ubuntu on a Windows computer. I get the following error when I run the freeview command : This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb. Aborted Any ideas? Best, John _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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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Freesurfer September 2024