Freesurfer

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30064 discussions

TIV from manually corrected aseg+aparc.mgz
by Daniela Vecchio 19 Apr '23

19 Apr '23

External Email - Use Caution Hi FreeSurfer Developers, For our study we had to manually correct some recon-all outputs due to some ROIs underestimation. For the purpose we manually edited the aparc+aseg.mgz file using the "voxel edit” command from Freeview. Then we use the mri_segstats command to extract volumes from the corrected aparc+aseg.mgz file. However, from the MRI_segstats we didn’t obtain a new TIV value. I want to ask if the TIV value is computed using the parcellation files (like aseg+aparc one) or instead using the brain.mgz file. How can I check that the TIV value reported in aseg.stats was unaffected from the underestimation we had to correct? Please find below the command we use to compute volumes from the corrected aseg+aparc file: mri_segstats --seed 1234 --seg /Applications/freesurfer/7.1.1/subjects/CorrectedSegmentations/${subj_id}.mgz --sum /Applications/freesurfer/7.1.1/subjects/${subj_id}/stats/AllVolumes.stats --pv /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --empty --brainmask /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/freesurfer/7.1.1/AreasList.txt --subject ${subj_id} Thank you for your support! Daniela

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is it possible to run a longitudinal study on 2 "-base" images?
by KennethSPrice 19 Apr '23

19 Apr '23

External Email - Use Caution Helloo, I have 2 sets clinical scans on a single subject that I put through Synth_SR. The Synth_SR tutorial suggests that if you have T1, T2, and FLAIR scans, you might want to average the number of voxels when doing ROI analysis. I want to apply this logic to cortical analysis. My idea is to "average" the cortex of T1, T2, and FLAIR scans from year 1 and year 2 using the longitudinal pipeline. Then I'd like to compare the "-base" images from both sets. Previously, when I've tried using the "-base" images in a study, I get the error that says something to the effect of "It appears that this subject ID is an existing base/template from longitudinal processing (-base): xxxx. If you are trying to re-run a -base template you need to pass the -base and all -tp flags:...." So, is it possible to do a longitudinal analysis on 2 "-base" images, or is there a different method you might suggest? Thank you all.

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License key
by Mohammad Amin Khodadadegan 19 Apr '23

19 Apr '23

External Email - Use Caution Hello could you please guide me where I should copy the license.txt file in Linux Ubuntu There is no installation demo video for Linux and I am totally confused I couldn't install freesurfer, not only the DEB file but also tar.gz . Unfortunately, all the instructions are for MacOS. Please guide me to follow your lead. -- *Kind regards,* *Khodadadegan M.A,* *Medical Doctor* *Mashhad University Of Medical Sciences* *Mashhad* *Iran*

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freesurfer download zip password
by Parmaksiz, Deniz 19 Apr '23

19 Apr '23

External Email - Use Caution Hi, I'm trying to download FreeSurfer and run it on VirtualBox but can't expand the 7zip file on WinRAR because I don't have a password. I saw 'brain2009' suggested online but WinRAR gives an error message saying the file is either corrupted or it's the wrong password when I try that. The wiki says to contact you & I would really appreciate help with this -- thanks! Best, Deniz

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Fwd: Password to VirtualMachine request
by Gromki Hados 19 Apr '23

19 Apr '23

External Email - Use Caution Hi, I would like to kindly ask you for the password for FreeSurfer 7.2.0 Virtual Machine. I tried using old password (brain.map), but that doesn't work anymore. Also, is there a possiblity of getting sudo password? It was quite annoying to work on previous version without it. Thank you in advance! Best regards, Jakub Wojciechowski

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Re: [Freesurfer] ABORT error when running freeview
by fsbuild 18 Apr '23

18 Apr '23

External Email - Use Caution From your first email, w/o seeing more of the crash log, I would infer something went wrong communicating with the Xming server, which caused the thread to abort.  WSL continues to be a moving target and people have found the XMing settings for WSL1 no longer work with WSL2.  Some WSL users have switched to using MobaXterm (https://secure-web.cisco.com/1zZzK3bvGd5zsB2uABu9OZeWvaxLdkpnrA0kBfX1S3S3ND…) and find it easier to configure compared XMing, though I have not tried it.  Others have switched to using the VirtualVox VM we provide with freesurfer pre-installed (https://secure-web.cisco.com/1fhOwedIcHgfE4tyeSK9G0oaBhabx6_ZVJc7Vr6kaXK3Uy…) since the X-Server runs in the VM (no 3rd party X-server to install and configure settings for).   While that VM runs Ubuntu 18 out of the box, you could uninstall freesurfer, upgrade to Ubuntu 22, and then install the freesurfer 7.3.2 Ubuntu 22 .deb file into it. - R. On Apr 18, 2023, at 19:00, Keith E Moore <kem1(a)stanford.edu> wrote:        External Email - Use Caution        Okay, so it does look like it is the LIBGL bandwidth.  I went back and downgraded WSL to version1.0 (non-VM).  Yes, a bit draconian, but wanted to see if this was a lack of shared memory accessibility.Used:Cmd> wsl –set-version ubunto 1 Then reran and got the expected image: $<image001.png> So looks like there is an issue when interacting with X11 servers when the client  is in a VM?  Anyway,  I’ll work with  this… but would be grateful if there’s a better configuration. Keith From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh..harvard.edu> On Behalf Of Keith E MooreSent: Tuesday, April 18, 2023 3:21 PMTo: Freesurfer support list <freesurfer@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] ABORT error when running freeview         External Email - Use Caution        Okay, found one issue.  My .bashrc had:export LIBGL_ALWAYS_INDIRECT=1I then went to unpacked tutorial  and ran: $ 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 and got:   <image002.png> So most is working except the image isn’t showing… any ideas? Keith Moore From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr..mgh.harvard.edu> On Behalf Of Keith E MooreSent: Tuesday, April 18, 2023 2:53 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] ABORT error when running freeview         External Email - Use Caution        Hi, when I try to use freeview on ubuntu under WSL, I’m getting a brief show of a X window and then an ABORT. I’m running in ubunto 22.04 (jammy)  under WSL on windows using an Xming 6.9.0.31xMing is configured with a X11 server on localhost:0.0 I did a clean install of ubunto using:Cmd> wsl –install ubuntu Then in ubunto:$ sudo apt update -y$sudo apt-get upgrade -y$sudo apt install x11-apps$sudo apt install xterm I installed freesurfer using:$sudo apt install ./freesurfer_ununtu22-7.3.2_amd64.deb Then added:$export DISPLAY=”:0.0”$export FS_LICENSE=<location of my license file>$export FREESURFER_HOME=/usr/local/freesurfer/7.3.2$export XDG_RUNTIME_DIR=/home/<myaccount>/.xdg$export SUBJECTS_DIR=<location of subjects>$source $FREESURFER_HOM/SetUpFreeSurfer.sh $ freeviewAborted $sudo apt install gdb$gdb freeview(gdb) run An Xwindow pops up which is blank/black that has the title “FreeView”. And gdb reports: <image003.png>  I’m sort of stuck… any idea what to try next? Keith Moore    _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ABORT error when running freeview
by Keith E Moore 18 Apr '23

18 Apr '23

External Email - Use Caution Hi, when I try to use freeview on ubuntu under WSL, I'm getting a brief show of a X window and then an ABORT. I'm running in ubunto 22.04 (jammy) under WSL on windows using an Xming 6.9.0.31 xMing is configured with a X11 server on localhost:0.0 I did a clean install of ubunto using: Cmd> wsl -install ubuntu Then in ubunto: $ sudo apt update -y $sudo apt-get upgrade -y $sudo apt install x11-apps $sudo apt install xterm I installed freesurfer using: $sudo apt install ./freesurfer_ununtu22-7.3.2_amd64.deb Then added: $export DISPLAY=":0.0" $export FS_LICENSE=<location of my license file> $export FREESURFER_HOME=/usr/local/freesurfer/7.3.2 $export XDG_RUNTIME_DIR=/home/<myaccount>/.xdg $export SUBJECTS_DIR=<location of subjects> $source $FREESURFER_HOM/SetUpFreeSurfer.sh $ freeview Aborted $sudo apt install gdb $gdb freeview (gdb) run An Xwindow pops up which is blank/black that has the title "FreeView". And gdb reports: [cid:image001.png@01D97205.3B00A040] I'm sort of stuck... any idea what to try next? Keith Moore

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Loading and editing volumetric .annot in Matlab
by Len Jacob 18 Apr '23

18 Apr '23

External Email - Use Caution Dear Freesurfer enthusiasts, I would like to load a volumetric aparc.annot file into Matlab with the goal of editing the color information for certain ROIs in order to convey some group-level results in the subcortex. I've previously done this for cortical surfaces by loading lh.aparc.annot (and rh.aparc.annot), but I now need to convey surbcortical results, and read_annotation does not work for the volumetric aparc.annot. I assume write_annotation would not work either. All the information I have been able to find relating to modifying a .annot and creating custom colortables has been for surface data. Any help in getting this done in the subcortex would be appreciated. Best regards, Len -- Leandro P. L. Jacob, Ph.D. (he/him) Postdoctoral Associate at the Lewis Lab Biomedical Engineering Department, Boston University

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How to convert segmentSubjectT1T2_autoEstimateAlveusML.m to matlab binary file?
by Nobuaki Hondo 18 Apr '23

18 Apr '23

External Email - Use Caution Dear FS team, I am using FreeSurfer (v7.1.1) and would like to change the internals of segmentSubjectT1T2_autoEstimateAlveusML for my own analysis. The source code is available, but I don't know how to convert segmentSubjectT1T2_autoEstimateAlveusML.m to Matlab binary. I would appreciate it if you could enlighten me. Best regards, Nobuaki Hondo

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Re: [Freesurfer] Freesurfer crash question
by fsbuild 17 Apr '23

17 Apr '23

External Email - Use Caution Are you using a second monitor, i.e., additional monitor besides the primary one?   There have been issues with images being displayed properly when using multiple monitors with MacOS.  I would first try everything on the primary monitor (disconnect any second monitor). If you have not tried running freeview directly from the command line, e.g., to display a volume, then please try the following.  Open a new terminal window and run the bash shell, $ bash… prompt will change ...$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output with variable settings … … then see if freeview opens an empty window … $ freeview … then try to display one of the existing volumes in the distribution, $ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz If you still see a blank screen, then try setting, $ export QT_DEBUG_PLUGINS=1 … and run the command again.  The output may be useful. - R. On Apr 17, 2023, at 14:19, He, Julian H <HEJ(a)helix.mgh.harvard.edu> wrote:<freesurfercrash.pdf>

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