Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

89 participants
132 discussions

matlab 2019b and brainstem substructures analysis
by tulu＠ms36.hinet.net 08 Oct '22

08 Oct '22

External Email - Use Caution Dear Freesurfer experts, I will analysis brainstem structure and I use Freesurfer 7.2 version and maltab 2019b. I wonder if I need to install Matlab R2014b runtime or how to run hippocampal subfield/brainstem module by matlab2019b Thanks your help Jung Lung Hsu

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pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Shen Vivien 08 Oct '22

08 Oct '22

External Email - Use Caution Dear freesurfer developer: Thank you for your great tool and communication platform. I am writing to ask for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z, as I failed to find it anywhere. Could you kindly provide it? Many Thanks! Wenwen

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Parcellating Individuals using Yeo17Networks Atlas
by Remiszewski, Natalie 07 Oct '22

07 Oct '22

External Email - Use Caution Hi all, I have a dataset of structural MRIs that I have previously used FS on to parcellate into the DKT and Destrieux atlases. I am interested in parcellating and getting cortical thickness values using the yeo17networks atlas. Is there a way to modify recon-all so that i can get individual yeo17 data for each subject? Thank you! Best, Natalie Remiszewski Graduate Student Trainee University of Alabama at Birmingham Kraguljac Lab

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Re: [Freesurfer] Freeview does not show images
by fsbuild 07 Oct '22

07 Oct '22

External Email - Use Caution Did it say the driver was installed successfully?   I’m wondering if the driver did not install because it does not support your machines hardware for some reason.  But it should tell you if it cannot be installed. You can tell if the DCH driver is installed by following the instructions here,https://secure-web.cisco.com/1C5iHX14FwFkb0bd5IYlzilnGkZNKBRhHFB5E1e8V… There is more info about it here,https://secure-web.cisco.com/1OnUvmRVhRWfRd2WCZXsandn42tB-a7ROvNPXbkZS… - R. On Oct 7, 2022, at 06:05, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        Hi  Ruopeng,I tried to run the glxgears command in the WSL Ubuntu subsystem, but it doesn't show me the gears. I am having the same issue as this thread linked here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NxVL-emVuHw_jOzG4gXfcbpKLhoo9hS4C5IwC… I followed the advice and downloaded the latest Intel Graphics Driver, but this did not seem to fix the issue for me. I also looked at the corresponding debian package installer in accordance with my ubuntu version, and the same error occurs. How can I add a 3D accelerator or GPU acceleration so that the glxgears command can show me the gears?Thanks for your help and time.Sincerely,JustinaOn Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Are you able to run glxgears command? Do you see spinning gears?RuopengOn Oct 6, 2022, at 4:28 AM, 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(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1x2O2S2I-mf4HqnIK9_KstdCRE_wrCYlZRAFyk… mailing listFreesurfer@nmr.mgh..harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1TH-a_ARr0KQ1PoZEkN8WQN8Bk3ci8v4cWfSc3… 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/11TjdGy9B7gzRP3B7lBnlaCwFqv13mfF9heyLn… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HcGt3lm_5mwfaxmqwtlQ5ekQZRDmp28yuUB4e…; ._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview does not show images
by Justina Lee 07 Oct '22

07 Oct '22

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/.bashrc* Then 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

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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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Freesurfer October 2022