Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Password for virtual machine FS_7_2_0_ubuntu_18_04_06
by Riccardo Accetta 02 Jan '23

02 Jan '23

External Email - Use Caution Hi can I have the password for the virtual machine that I have downloaded ? Thanks Best Regards Riccardo Accetta

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Re: [Freesurfer] Freeview crashes after installing the software
by fsbuild 02 Jan '23

02 Jan '23

External Email - Use Caution Please try the following with the latest 7.3.2 release if you are not already running 7.3.2.  The release page is https://secure-web.cisco.com/1zn1v_OOPT0MJ0XxXSk4mw5hbeQD4yegZ0PSsC… the link to the .pkg file is https://secure-web.cisco.com/17qSx4asejqc1SOr4BdhhxtQLAqSTPmbMEBpF2… 1) Install the 7.3.2 release listed above.  It will be installed as /Applications/freesurfer/7.3.2 2)  Open a new terminal window and run the bash shell as, $ arch -arm64 /bin/bash 3) Set FS_LICENSE to point to the license.txt file you downloaded after registering via the online form at https://secure-web.cisco.com/1hvYfe1hO7ZqQEnaogRQmpJSBSH4ZqL7YpQWNvh19EOSXJ…  For example, it could be in your home directory as $HOME/license.txt.  It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read. $ ls $HOME/license.txt/Users/<your userid>/license.txt$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)youremail.something     <— email you used to register with 4) Setup the environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ 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       /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects MNI_DIR           /Applications/freesurfer/7.3.2/mni 5) Try running freeview from the command line w/o any arguments to see if it opens an empty window, $ freeview 6)  If that worked, quit freeview and then run freeview from the command line again to open one of the provided volumes in the 7.3.2 release, $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz 7) If that worked, then try running freeview from the command line on one of your own volume or surface files. - R. On Dec 30, 2022, at 12:55, Seyedeh Nasim Adnani <sza0127(a)auburn.edu> wrote:        External Email - Use Caution        Hello, I have a MacBook Pro with Ventura 13.1 OS, 64 GB, SMC Apple M1 Max.I recently started installing the freesurfer software but unfortunately, a simple volume loading into the freeview crashes without displaying any image.I have tried installing various python versions (2,3) and modifying the PATH but nothing seems to help. Now, I wonder if the software is compatible with my mac. Is there any way I can make it work on my system? Many thanks in advance for your help. Best,Nasim Adnani,Sza0127@auburn.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Password for FreeSurfer project
by Sangeen Khan 01 Jan '23

01 Jan '23

External Email - Use Caution Hi, I’m interested in the freesurfer project. Can I have the password to unzip the virtual machine FS_7_2_0_Ubuntu_18_04_06.ova.7z? Thanks Sangeen khan

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Freeview crashes after installing the software
by Seyedeh Nasim Adnani 30 Dec '22

30 Dec '22

External Email - Use Caution Hello, I have a MacBook Pro with Ventura 13.1 OS, 64 GB, SMC Apple M1 Max. I recently started installing the freesurfer software but unfortunately, a simple volume loading into the freeview crashes without displaying any image. I have tried installing various python versions (2,3) and modifying the PATH but nothing seems to help. Now, I wonder if the software is compatible with my mac. Is there any way I can make it work on my system? Many thanks in advance for your help. Best, Nasim Adnani, Sza0127(a)auburn.edu

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Help: Aparcstats and asegstats not working
by vittal korann 29 Dec '22

29 Dec '22

External Email - Use Caution Hi Freesurfer experts, I am trying to collate all morphological parameters like thickness, area, volume, etc. When I tried executing the command " asegstats2table --subjects Met001 met002 .... --hemi lh --meas area --tablefile Area_aseg_stats.txt ", it failed and I got the below error which is highlighted. File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')? File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')? I am using the Freesurfer version6 and ubuntu 20.04. A similar error was reported in the forum and I also tried the suggested solution by setting python2.7 as the default version. However, nothing has worked out for me. Any help would be highly appreaciated. Thanks, Vittal

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Freesurfer Image Attribute
by Kalluvila, Aryan 29 Dec '22

29 Dec '22

Good morning Freesurfer Team, Is there a certain freesurfer version that needs to be installed in order to get the image attribute? For example, I have freesurfer ubuntu linux 7.2.0 installed but I can't pass through the function fs.Image(xxx) without getting an error. Please let me know. Thanks, Aryan

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password for virtual machine request
by Riccardo Accetta 29 Dec '22

29 Dec '22

External Email - Use Caution Hi, I'm interested on freesurfer project can I have the password to unzip the virtual machine ? Thanks Riccardo Accetta

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Password for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Steven Keller 28 Dec '22

28 Dec '22

1 0

Training in Advanced Statistical Methods in Neuroimaging and Genetics, April 2023
by ROBERT CARY WELSH 27 Dec '22

27 Dec '22

External Email - Use Caution Hi Folks, Our NIH-funded course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”, will be held in-person in Salt Lake City, UT, from April 3 – April 14, 2023. This is a course geared to advanced undergraduate students graduate students, postdocs, and junior faculty. Topics include: Bayesian methods of functional connectivity and activation, longitudinal modeling, network neuroscience, polygenic risk scores, multimodal modeling and predictive modeling. The course is a mix of lectures and hands-on computer labs. Our main lecturers include: Martin Lindquist, Johns Hopkins University Mandy Mejia, Indiana University Rick Betzel, Indiana University Anna Docherty, University of Utah To read more about the course and to apply please see: https://secure-web.cisco.com/1mMCzFjpIVXxHtqbxdAnyxeb_su-nbB4mp7sVKpBybhUAU… For more information please write : advancedstatisticscourse(a)utah.edu<mailto:advancedstatisticscourse@utah.edu> Best, Robert Welsh and Anna Docherty

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Pass code
by skalytta＠smail.uni-koeln.de 25 Dec '22

25 Dec '22

External Email - Use Caution Hello, could you please send me the pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z? Thank you! Best regards, Sebastian

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