Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] Freeview does not show images
by fsbuild 06 Oct '22

06 Oct '22

External Email - Use Caution I don’t think you told us what you installed for freesurfer in WSL.   The freesurfer installation should match the version of Ubuntu Linux that WSL installed. You can check the Ubuntu OS version in the Ubuntu terminal window with, $ cat /etc/os-releaseNAME="Ubuntu"VERSION="20.04..4 LTS (Focal Fossa)”. <—- Ubuntu OS version = 20ID=ubuntuID_LIKE=debianPRETTY_NAME="Ubuntu 20.04.4 LTS"VERSION_ID="20.04"HOME_URL="https://secure-web.cisco.com/1bVGj42N9EXVJFRZ7YL0IHj3ZYnjuVnNPLHNWkT-3uhiq6…"SUPPORT_URL="https://secure-web.cisco.com/12UtwR8986v4WnSkHQkzTHdLViFU2xy4D4gPieyqjFBGaU…"BUG_REPORT_URL="https://secure-web.cisco.com/1ovllB_ySt3ww3AwjGhOIt_eu_N2HW4iWf5szA8QTOw55-…"PRIVACY_POLICY_URL="https://secure-web.cisco.com/1gsSaM6y5sGY58Zoe__dEZ5uF1C7Q91HlD5GBMyNhKdRRc…"VERSION_CODENAME=focalUBUNTU_CODENAME=focal With the above version info, you can use the debian package installer (.deb file), e.g., from https://secure-web.cisco.com/1suBrY-ijWwnSebRIO5a6tmmiUPrI9YyHka5F3mVaW4Enb…, that matches your version of Ubuntu.  For Freesurfer 7.3.2 the choices are: freesurfer_ubuntu18-7.3.2_amd64.debfreesurfer_ubuntu20-7.3.2_amd64.debfreesurfer_ubuntu22-7.3.2_amd64.deb For the output above, you would choose freesurfer_ubuntu20-7.3.2_amd64.deb to match the version of Ubuntu Linux. … cd in Ubuntu linux to where you downloaded or copied in the freesurfer_ubuntu20-7.3.2_amd64..deb file …… and install it with ...$ sudo apt install ./freesurfer_ubuntu20-7.3.2_amd64.deb … and if the install succeeds then freesurfer would be installed under …/usr/local/freesurfer/7.3.2 … and to remove the install above you would do …$ sudo apt remove freesurfer If you didn’t use the “apt install” command above to install freesurfer, then I would remove your current copy of the ./freesurfer tree, and do the “apt install”.  Then you could source the freesurfer setup script and try running freeview again. Microsoft can change the WSL environment without notice when your Windows machine updates.  The version of Ubuntu linux installed in WSL depends upon when you set it up on your machine.  We try to troubleshoot issues users report back to us, but we can’t always remotely debug every interaction between WSL, different X servers (X-ming, Moba Xterm) and your machines graphics card.   We have written up some of workarounds at the bottom of this page, https://secure-web.cisco.com/1Wk9iTNOO9n-TGjUWv3BghCeFjAi82pV6d2…   But some users are not able to get a 3rd party X-server running on Windows to work with every graphics application they run in WSL.   A simpler alternative is to use the VirtualBox VM as it has both freesurfer and an X-server pre-installed matching the OS provided in the VM. - R. On Oct 6, 2022, at 04:28, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom this may concern and can help, I am currently trying to run Freeview under the Windows Subsystem Linux System. I can successfully download and open images, but nothing seems to be showing on my end (see image attached at the end). In order to find out what is preventing the X-server from correctly displaying graphics, I have tried to run the $ xeyes command and the eyes pop up, meaning that the X-windows server is working fine.Upon checking the WSL Version, I am currently using the WSL version 2.I have entered the two commands as follows:$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrcThen I exited Ubuntu, and tried to run freeview again (attempting to open a data file T1.mgz.) This still did not produce any image in freeview, although it opened it up. I tried changing the window, contrast, and brightness but to no avail. Is there another solution?Terribly sorry and thank you so much for your time.Sincerely,Justina <Freeview image display.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1
by fsbuild 05 Oct '22

05 Oct '22

External Email - Use Caution You could try running FS 5.1 on Ubuntu 12 using either a container or VM, but I’m not aware of a container with Freesurfer 5.1 already installed. I would try the VirtualBox VM with Freesurfer 5.3 and see if that works.  That is a known to be good image of the OS with everything installed for at least FS 5.3 to run.   You could first make a snapshot of the VM and then try installing FS 5.1 in it and see if it works.  If you have IT staff, they should be able to help you with doing this if you are not familiar with VirtualBox. - R. On Oct 5, 2022, at 15:07, Leema_Murali(a)eisai.com wrote:        External Email - Use Caution        Thank you so much for a detailed explanation. I have never tested FS 5.1 previously. This is my first time testing this version in a docker container. I’m not sure what older version of OS that should be used. Is there a docker base image available for FS 5.1 like it’s there for FS 7.2.. Regards,Leema From: fsbuild <fsbuild@contbay.com> Sent: Wednesday, October 5, 2022 2:54 PMTo: freesurfer@nmr.mgh..harvard.eduCc: Leema Krishna Murali <Leema_Murali@eisai.com>Subject: Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5..1 Security First: External email, use caution clicking links or opening attachments.It looks like you are running into undefined symbols when running on Ubuntu 16.   You may need to use an older version of the OS.  I say that because we have an Ubuntu 12 VM with Freesurfer 5.3 that runs on VirtualBox available from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-V…   And FS 5.1 predates FS 5.3. We post a note you should be aware of about changing the operating system you run freesurfer on: Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). I interpret that to mean you should try and run FS 5.1 on the version of the OS you previously ran it on.  Otherwise, you may not get the same floating point output from running your existing test subjects. So as Paul mentioned, you can use a container, a virtual machine (VM) or any virtualization scheme to run FS 5.1 on am older version of the OS, and host the container, VM, etc. on Ubuntu 18.   Ubuntu Linux has its own built-in virtualization called QEMU.   I would at least start with whatever OS you previously ran FS 5.1 on as the reference. - R. On Oct 5, 2022, at 14:36, Leema_Murali@eisai.com wrote:         External Email - Use Caution         Hi Paul, Thank you for your response. I did try running FreeSurfer inside a docker derived from Ubuntu 16.04. Now there is no license invalid error. But I’m facing another error with regard to Segmentation. Please find the below screenshot.. <image002.png> Thank you,Leema From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wighton, PaulSent: Wednesday, October 5, 2022 11:30 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [EXTERNAL] Re: [Freesurfer] Error while testing FS version 5.1 Security First: External email, use caution clicking links or opening attachments.Hi Leema, This is a known issue.  It has to do with the behaviour of the crypt() function provided by glibc, which has changed in more recent versions of ubuntu.  We don't have a solution for it at this time, unfortunately. If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism should work, or you could upgrade your version of FreeSurfer.  If neither of those options are possible, you could run FreeSurfer inside a docker or singularity container derived from ubuntu 16.04. -Paul From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Leema_Murali@eisai.com<Leema_Murali@eisai.com>Sent: Wednesday, October 5, 2022 8:43 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh..harvard.edu>Subject: [Freesurfer] FW: Error while testing FS version 5.1         External Email - Use Caution        Hello FreeSurfer Developers, I’m trying to use Freesurfer version 5.1 for my work. I get errors based on invalid license even though I have provided the right license within $FREESURFER_HOME/.license Is there a specific way to define the license file for 5.1 version. I have been using the latest version before and I had just added the license.txt with $FREESURFER_HOME. Please can anyone help me to troubleshoot this  issue. Platform: Ubuntu 18.04Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0recon-all.log: see attached <image003.png> Looking forward for you reply. Thank you,Leema[This e-mail message may contain privileged, confidential and/or proprietary information of Eisai. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.] _______________________________________________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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Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1
by fsbuild 05 Oct '22

05 Oct '22

External Email - Use Caution It looks like you are running into undefined symbols when running on Ubuntu 16.   You may need to use an older version of the OS.  I say that because we have an Ubuntu 12 VM with Freesurfer 5.3 that runs on VirtualBox available from https://secure-web.cisco.com/1OwyjJ1rTGJ_2TzRiqQk1sQK1uz8hOtzOw5o…;   And FS 5.1 predates FS 5.3. We post a note you should be aware of about changing the operating system you run freesurfer on: Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). I interpret that to mean you should try and run FS 5.1 on the version of the OS you previously ran it on.  Otherwise, you may not get the same floating point output from running your existing test subjects. So as Paul mentioned, you can use a container, a virtual machine (VM) or any virtualization scheme to run FS 5.1 on am older version of the OS, and host the container, VM, etc. on Ubuntu 18.   Ubuntu Linux has its own built-in virtualization called QEMU.   I would at least start with whatever OS you previously ran FS 5.1 on as the reference. - R. On Oct 5, 2022, at 14:36, Leema_Murali(a)eisai.com wrote:        External Email - Use Caution        Hi Paul, Thank you for your response. I did try running FreeSurfer inside a docker derived from Ubuntu 16.04. Now there is no license invalid error. But I’m facing another error with regard to Segmentation. Please find the below screenshot. <image002.png> Thank you,Leema From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard..edu> On Behalf Of Wighton, PaulSent: Wednesday, October 5, 2022 11:30 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [EXTERNAL] Re: [Freesurfer] Error while testing FS version 5.1 Security First: External email, use caution clicking links or opening attachments.Hi Leema, This is a known issue.  It has to do with the behaviour of the crypt() function provided by glibc, which has changed in more recent versions of ubuntu.  We don't have a solution for it at this time, unfortunately. If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism should work, or you could upgrade your version of FreeSurfer.  If neither of those options are possible, you could run FreeSurfer inside a docker or singularity container derived from ubuntu 16.04. -Paul From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Leema_Murali@eisai.com<Leema_Murali@eisai.com>Sent: Wednesday, October 5, 2022 8:43 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] FW: Error while testing FS version 5.1         External Email - Use Caution        Hello FreeSurfer Developers, I’m trying to use Freesurfer version 5.1 for my work. I get errors based on invalid license even though I have provided the right license within $FREESURFER_HOME/.license Is there a specific way to define the license file for 5.1 version. I have been using the latest version before and I had just added the license.txt with $FREESURFER_HOME. Please can anyone help me to troubleshoot this  issue. Platform: Ubuntu 18.04Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0recon-all.log: see attached <image003.png> Looking forward for you reply. Thank you,Leema[This e-mail message may contain privileged, confidential and/or proprietary information of Eisai. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.] _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FW: Error while testing FS version 5.1
by Leema_Murali＠eisai.com 05 Oct '22

05 Oct '22

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to use Freesurfer version 5.1 for my work. I get errors based on invalid license even though I have provided the right license within $FREESURFER_HOME/.license Is there a specific way to define the license file for 5.1 version. I have been using the latest version before and I had just added the license.txt with $FREESURFER_HOME. Please can anyone help me to troubleshoot this issue. Platform: Ubuntu 18.04 Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 recon-all.log: see attached [cid:image001.png@01D8D895.A24160F0] Looking forward for you reply. Thank you, Leema [This e-mail message may contain privileged, confidential and/or proprietary information of Eisai. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.]

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Re: [Freesurfer] Segmentation fault: 11
by fsbuild 05 Oct '22

05 Oct '22

External Email - Use Caution Hello Priya, It could help to know,- the version of freesurfer you installed, e.g., the latest 7.3.2 release from https://secure-web.cisco.com/1zdcvVhqKzcbDdvruGd5f9eNe1UebLwxcHQN… if you used the pkg installer file, https://secure-web.cisco.com/1kDieI9mdZudxJbpCFL6WFWngUIQhFugSux… what version of MacOS you are running- if you are on an Intel Mac or a new Mac with an M1 or M2 chip. Please make sure you have registered and obtained the freesurfer license.txt file by filling out the form, https://secure-web.cisco.com/1fpZEOUr_MAQGgEoaIOkzRF-3qUqa6N-GPo… The thread you referenced, https://secure-web.cisco.com/1D0s4CKkxCu5d6CQKJUyf4knHMaxq…, showed the crash went away for a user with a MacBook Pro if they unplugged their external monitor.  This is - or at least was - a known problem with a 2nd monitor causing a segfault when trying to run some graphics programs.  So try unplugging any external monitor if you are using a Mac laptop. I would try explicitly running the bash shell in your terminal window, but typing “bash” at the terminal prompt.  You should then see the output, $ bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://secure-web.cisco.com/1weI0CySFCptz62exS6gCfA2Ymaa7qVQzIZURPdDJ1Yz2d…; You can then set FS_LICENSE in your environment to point to the license.txt file.  You can put license.txt in your home directory, e.g., wherever that path is, userid@hostname:~> echo $HOME/Users/priya userid@hostname:~> export FS_LICENSE=$HOME/license.txtuserid@hostname:~> cat $FS_LICENSE< output deleted - just make sure the environment variable points to license.txt > Then setup the fressurfer environment, e.g., for the 7.3.2 release installed with the .pkg file, userid@hostname:~> export FREESURFER_HOME=/Applications/freesurfer/7.3.2userid@hostname:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.3.2 FSFAST_HOME       /Users/developer/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Users/developer/freesurfer/subjects TUTORIAL_DATA     /Users/developer/tutorial_data MNI_DIR           /Users/developer/freesurfer/mni WARNING: /Users/developer/freesurfer/fsl_507/bin does not exist. FSL_DIR           /Users/developer/freesurfer/fsl_507 userid@hostname:~> which freeview/Applications/freesurfer/7.3.2/bin/freeview … try running freeview with no argument to see if it brings up an empty window … userid@hostname:~> freeview … try displaying a simple volume … userid@hostname:~> freeview $SUBJECTS_DIR/bert/mri/brain.mgz Let us know how it goes. - R. On Oct 5, 2022, at 03:11, priya padma <priya(a)phenomx.ai> wrote:        External Email - Use Caution        Hello Team,I just installed freesurfer and freeview using the methods mentioned in MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JYUd4mMfSzih2QyO4E11xD88kcF1UC15qYki4… installation was successful and after creating the environment the freeview also opened but whenever I open any volume, freeview crashes and I get an error saying line 2:  6736 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"I followed the thread MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1LcCJqrQekIc5hnecCI_yYw-ueM-8XSvqnvS6V… tried to move the terminal to the main laptop screen but still I get the same error. I am unable to open the sample data given along with freesurfer.Could you help me with this issue?-- Best RegardsPadma PriyaAI Developer PhenoMx, Inc.priya(a)phenomx.ai | (+82)10-5405-2685_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Password for FreeSurfer VirtualBox VM Images
by zhenyi 05 Oct '22

05 Oct '22

External Email - Use Caution Dear FreeSurfer experts, I would like the password to unzip the virtual machine FS_7_2_0_ubuntu_18_04_06.ova.7z. Thanks a lot. Best regards

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Segmentation fault: 11
by priya padma 05 Oct '22

05 Oct '22

External Email - Use Caution Hello Team, I just installed freesurfer and freeview using the methods mentioned in https://secure-web.cisco.com/1oeEk1V3fGDlcuYEIm1RFYCYdQcU2m3TJysRGz7NAzZIOM… the installation was successful and after creating the environment the freeview also opened but whenever I open any volume, freeview crashes and I get an error saying line 2: 6736 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" I followed the thread https://secure-web.cisco.com/1Xm7JHZ-l0iAQ6540xdJyuY8nR4ldJU2U31IejPX9O93yn… and tried to move the terminal to the main laptop screen but still I get the same error. I am unable to open the sample data given along with freesurfer. Could you help me with this issue? -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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How to Verify That Cortical Surface Orientation Values are Accurate?
by Bansal, Krishan Chandra 04 Oct '22

04 Oct '22

External Email - Use Caution I have created a volume which is supposed to have the cortical surface orientation with respect to b0 at each voxel. To do this I got the 6 frame overlay file from mris_convert. Then I isolated the first 3 values from each row in Matlab to create an Nx3 matrix, then from this I calculated the angle between each row vector and the b0 vector (which was just [0 1 0]) using the usual angle between two vectors formula. The result was an Nx1 matrix.I then saved it as an .mgh surface file (using save_mgh) and projected it back onto the original volume using surf2vol. I believe that I did this correctly, however the professor that I am developing this method for told me he wants me to verify that the results are correct. He was not very specific in how to do this, all he told me was that I could use volumes of the individual scanner x,y,z angles to help me figure out if my b0 results are right. What I assume he meant is: since the b0 axis goes vertically down the middle of the brain when in coronal view I can tell if the b0 angles are correct by seeing where the cortical surface is with respect to the z scanner direction and seeing if the b0 angle at the corresponding location makes sense. My problem is that I can’t tell if my results make sense. In theory I believe that at the locations where the cortex appears to be orthogonal to the B0 (z scanner) axis, the overall B0 angle of the cortical surface should be closer to 90 degrees. I still don’t understand what pattern I should be seeing in the values of the z scanner volume compared to the b0 angles volume. Comparing my z scanner volume results to the B0 angle volume the only pattern I can see is that the cortical surface with respect to B0 is closer to 90 degrees when the z scanner volume is closer to 0 degrees. No B0 angle I got is actually greater than 89 though. I can’t tell if this is the right pattern or enough to verify the results in the way the professor I’m working for wants. Any help here would be GREATLY appreciated. I can send pictures of my results if someone wants to look at them.

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B0 distortion correction using 2. FSL epidewarp script
by Addison, Reuben 04 Oct '22

04 Oct '22

Hi, I am new to fsfast and I trying to create a field map using the AP and PA spin echo maps for B0 distortion correction using the FSL epidewarp script I have two fieldmaps PA_spinecho.nii and AP_spinecho.nii 1. First I want tow know if my code below is about right epidewarp.fsl --mag $dir/$subj/bold/fieldmap/ PA_spinecho.nii --dph $dir/$subj/bold/fieldmap/ PA_spinecho.nii --epi bold.nii.gz --tediff 2.46 --esp .69 --sigma 2 --vsm shiftmap.nii.gz --epidw bold_dw.nii.gz 1. If it is right, which output goes into my bold folder (“Shiftmap.nii”, I mostly suspect or “bold_dw.nii.gz” ) to be used for later preprocessing in FS-FAST 2. I want to know how to make this efficient for multiple subjects Reuben A.

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Re: [Freesurfer] Freeview does not display image
by fsbuild 04 Oct '22

04 Oct '22

External Email - Use Caution With regards to WSL, there is probably something preventing the X-server from correctly displaying graphics.  Instead of running freeview you could try a simpler command to test X-window graphics.  One command is “xeyes” which you can look for and try running in the Ubuntu terminal window by typing, $ which xeyes/usr/bin/xeyes$ xeyes If a window does not open displaying something like a pair of eyes then the X-windows server is not working correctly. There are 2 different versions of WSL, i.e. version 1 and 2.  The setup for the X-server can be different depending upon which version you are running.  You can try to find the version by typing the following command at the Windows command prompt.  The number under VERSION should be the version of WSL you are running. C:\Users\sam>  wsl -l -v   NAME     STATE     VERSION* Ubuntu   Running  2   <— means you are running WSL version 2 Down the bottom of this page are some instructions for setting up the Ubuntu shell environment for WSL, https://secure-web.cisco.com/1iKRwZpgN3zDuJlFspVtdJXrVV6ghp3nndYF… If you have not already run these 2 commands, then I would do so,  $ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrc Then exit your Ubuntu terminal window and start a new one so those settings take effect.  Then try running the “xeyes” command again to see if it works.  If it does work, then try running freeview again. With regards to trying to use the VM, if uncompressing the image is crashing then you may be running out of disk space.  You should check there is at least 40 Gig of free disk space in the location where you are trying to open the zip file. - R. On Oct 4, 2022, at 03:11, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        Hello R,Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows subsystem linux (WSL). I followed these instructions atMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl to download the WSL, X-server, and the freesurfer. Is it still possible to fix the problem here internally or should I follow the instructions sent from the link previously to download Virtual Box and run freesurfer in this way? I have been trying to open the zip file Ubuntu compressed image but it seems to keep crashing as I load it. I will keep trying if the first way aforementioned is not possible. Thank you and hope this has become alittle clearer. Sincerely,Justina On Mon, Oct 3, 2022 at 8:35 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Justina,We need to know what your setup is on Windows for running Linux in order to help with running freeview.  It reads like you are not using VirtualBox to run the Linux Ubuntu OS, I do not have VirtualBox installed ....So it’s not clear to me how you are currently running Ubuntu Linux on your Windows machine in order to run freeview or other freesurfer commands.  Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe you are connecting remotely to a linux machine via VNC or the like from your Windows machine ? If you don’t mind running freesurfer 7..2.0 (instead of the newest 7.3.2 release), there is a smaller version of the VM to download from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pDNeyyXnoU0PIQ7-rMdLh5tom581Kv0B3Mn8R…; with setup instructions under that link.   But you would still need to download and install VirtualBox on your Windows machine and then download and install the Freesurfer Software.- R.On Oct 3, 2022, at 09:35, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom that can provide any insight,I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the command freeview -v works, and I am able to run it smoothly.. When I try to open an mgz file, it runs fine, but I am unable to see anything.  I do not have VirtualBox installed and tried to take this advice from previous but I ran across the problem of downloading the course Virtual Machine. I do think that I do not need to download the VirtualBox and can continue using Ubuntu on Windows.What could be the issue with this? Should I be downloading the Virtual machine to run Freeview?Thank you so much for your time and I hope that my issue is not too big of a problem to solve.Sincerely,Justina_______________________________________________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(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/freesurferThe 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1R3cUq4RykRt6cPCE4lwjRCb05baj49mMr_HMN… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1deahsDR7bgySlDh-gqSvErXdDWMrr1x8nDI5a…; .-- Sent from Gmail Mobile_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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