Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

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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ERROR: flag i unrecognized
by Francisco Polito haro 17 Apr '23

17 Apr '23

External Email - Use Caution I'm trying to start a scan but I can't get it to start the recon process there, I get an error, I don't know what I'm doing wrong. with the test subject of BERT that marks the tutorial if it does, but with my file it doesn't, I attach the message and screenshot of the error that appears to me: [cid:828e9b1f-c7c6-4e72-8a91-72ae7c8b800c] Sin mas por el momento, reiterando mi subordinación y respeto, reciba un caluroso saludo. Sufragio Efectivo, No Reelección LFA Francisco Polito Haro CP 12915210

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FW: Freesurfer crash question
by He, Julian H 17 Apr '23

17 Apr '23

External Email - Use Caution Hello there, FS host, I had issue with the current version of freesurfer 7.3.2 Xquartz 2.8.5, MacOS 12.6.5 (adequate video Ram), installation appears fine, just crash as soon as I load data. See attached PDF of the crash screenshots) Thanks for your time. Please help. Julian From: He, Julian H Sent: Monday, April 17, 2023 2:07 PM To: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Subject: RE: Freesurfer crash question Thanks, Doug, Got it, I will do. Julian From: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Sent: Monday, April 17, 2023 2:05 PM To: He, Julian H <HEJ(a)HELIX.MGH.HARVARD.EDU<mailto:HEJ@HELIX.MGH.HARVARD.EDU>> Subject: Re: Freesurfer crash question Hi Julian, would you mind posting this problem to the FS email list? I think others will be able to answer it better than me. Make sure to include the version you are using. doug On 4/17/2023 2:03 PM, He, Julian H wrote: Good afternoon, Doug, Could you help me with this freesurfer crash issue, ( see attached PDF) Basically, I got an loaner -previous gen Mac Pro with video card, so I can finally give a try of your Freesurfer program, the installation went fine, I can launch the freeview, but as soon as I load a volume ( even from the subject sample data), the program will crash and quit. I can’t figure out why and don’t kwon what to do. Could you mind take a time to have a look and guide me through. Cheers Julian

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recommended change to FreeSurferEnv.sh
by Aaron Tanenbaum 17 Apr '23

17 Apr '23

External Email - Use Caution Recently FSL has changed the location of the bin directory they want you to use. The FreeSurfer setup script adds the old binary folder to the PATH not the new one. This is causing quite a bit of trouble for me. I made changes to the FreeSurferEnv.sh. I removed lines 440-446 and in its place I put the following. The echo line probably needs to be changed but it works. if [ -d $FSL_DIR/share/fsl/bin ]; then > export FSL_BIN=$FSL_DIR/share/fsl/bin > elif [ -d $FSL_DIR/bin ]; then > export FSL_BIN=$FSL_DIR/bin > else > if [[ $output == 1 ]]; then > echo "WARNING: $FSL_BIN does not exist."; > fi > fi

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FLAIRpial
by Jones, Richard 17 Apr '23

17 Apr '23

External Email - Use Caution We have noted some issues with the processing of the FLAIR images when using the FLAIRpial option with 7.3.2. In the attached PDF file the top row shows the FLAIR.prenorm.mgz images while the lower row shows the FLAIR.mgz images (the FLAIR.norm.mgz looked visually to be the same as the FLAIR.mgz image). There is some interesting contrast, particularly in the brainstem and around the corpus callosum, in the FLAIR.mgz image which is not apparent in the FLAIR.prenorm image, is this really something that one would expect from the image normalization? The recon-all log file is attached, as is the expert _options file used for this subject. We also saw the same effect when running 7.3.2 on a MacBook Pro fitted with a M1 Max processor and running the Ventura OS. Richard Jones Medical Physicist | Department of Radiology | Children's Healthcare of Atlanta * 404-785-5381 | *: richard.jones(a)choa.org<mailto:richard.jones@choa.org>

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