Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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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Running Freeview from Ubuntu
by Barsotti, Ercole 19 Sep '24

19 Sep '24

External Email - Use Caution 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

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BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
by Sambamoorthy, Sowmya 19 Sep '24

19 Sep '24

External Email - Use Caution Hello Freesurfer support, We have freesurfer/7.3.2 on CentOS7. This installation is working fine and the recons (recon-all -autorecon-pial -s $SUBJECT -parallel) run to completion. What we are trying to do: Upgrade OS to ROCKY Linux 8.10. and trying to make freesurfer/7.3.2 work to completion.The reason we are keeping 7.3.2 is to not add variance to the current project. What issue we are facing: <<snippet of the last few lines of the log below>> Reporting on 45 segmentations Using PrintSegStat mri_segstats done /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss/fmri102_005_rocky/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss; ln -s /opt/freesurfer/7.3.2/freesurfer/subjects/fsaverage; cd - ln: failed to create symbolic link './fsaverage': File exists #-------------------------------------------- #@# BA_exvivo Labels lh Wed Sep 11 17:06:02 CDT 2024 ------------------------------------------------------------------------- ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version ------------------------------------------------------------------------- Linux rocky8-sg.cvl.utdallas.edu 4.18.0-553.8.1.el8_10.x86_64 #1 SMP Tue Jul 2 17:10:26 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fmri102_005_rocky exited with ERRORS at Wed Sep 11 17:06:02 CDT 2024 More Context: 1. The same brain on Centos7 has no issues finishing recons. If needed, we can share logs for this. 2. We have tried adding some fsaverage switches as seen on a few support groups. "recon-all -autorecon-pial -s $SUBJECT -parallel --fs-subjects-dir $SUBJECTS_DIR". This does not seem to help and does not get past the initial phases of the run. Hope this helps in giving the picture of what we are attempting to accomplish. Please let me know if you have any questions. --Sowmya Sowmya Sambamoorthy Research Assistant (972) 883-3746 Functional Neuroimaging of Memory Laboratory [cid:image001.png@01DB0A8B.4D12C810] T H E U N I V E R S I T Y O F T E X A S A T D A L L A S

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Re: [Freesurfer] FreeSurfer License Error
by fsbuild 18 Sep '24

18 Sep '24

External Email - Use Caution  Since the last release of freesurfer 5.X in 2014, the encryption libraries on linux systems have changed such that the licenses downloaded for the current 7.X releases,https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads- cannot work with 5.X. If you were previously using 5.X on an old linux system, then you could run it with the license file that worked for you on that system in a container or VM running whatever that OS was - hosted on a current version of Linux like Rocky8, Ubuntu 22, etc. Otherwise, I suggest you download and install the 7.4.1 release via the link above.  The license file you downloaded should work with that. - R. On Sep 18, 2024, at 20:25, Barsotti, Ercole <john-barsotti(a)uiowa.edu> wrote:        External Email - Use Caution        Hi all, I've downloaded Freesurfer version 5.3 and signed up for a license. However, when I try to run the example: mri_convert sample-001.mgz sample-001.nii.gz I get the following error: ERROR: Invalid FreeSurfer license key found in license file /home/john/freesurfer/license.txt I'm not sure what to do here as I have the license file in the correct place and thought that I had obtained it correctly. Best, John_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer License Error
by Barsotti, Ercole 18 Sep '24

18 Sep '24

External Email - Use Caution Hi all, I've downloaded Freesurfer version 5.3 and signed up for a license. However, when I try to run the example: mri_convert sample-001.mgz sample-001.nii.gz I get the following error: ERROR: Invalid FreeSurfer license key found in license file /home/john/freesurfer/license.txt I'm not sure what to do here as I have the license file in the correct place and thought that I had obtained it correctly. Best, John

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Freesurfer