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Hello Nils, The first thing to check would be the video memory - I would try to give it the maximum. Another thing to check if that does not help is the CPU's. You could try increasing it from say 1 to 2 CPU's if you have a 4 core machine.
Take a look at the instructions we post for setting up a VM (and we also have an Ubuntu VM to download with FS 6 and 7 on it) - see,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 -R.
On May 23, 2020, at 14:16, Nils Böer <nils.tobias94@gmail.com> wrote: External Email - Use Caution Hello everyone,I'm new to Freesurfer and just got started. I have to analyze data which is already prepared (recon-all is already done). I can load my subjects data into freeview but when i start working on it, e.g. clicking through the slices my freeview (6.0) just freezes everytime without an error message. I can use the mouse to click or scroll through with the arrows but nothing happens on the screen anymore. Sometimes the display in freeview also starts to get gray and i can't see anything of the mri scan anymore (examples are in appendix).I'm running freesurfer 6.0.0 on a Win10 Computer with the Oracle VirtualBox using Ubuntu 18.04.4 LTS. I hope you can help me, i couldn't find anything related to this problem. Can it be related to problems with the RAM (Virtualbox is allowed to use 10GB of Ram).?Best regards,Nils-- Nils BöerResearch Assistant with Bachelor Degree (WHB) Psychology and MovementUniversity of PaderbornDepartment of Sports and HealthWarburger Str. 10033098 PaderbornRoom: Sp 1.401Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.deWeb: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/%C2%A0%C2%A0%C2%... display error and frozen.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi all, I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for hippocampal segmentation) that is lacking. How can I obtain it?
The file is a Matlab script:
segmentSubjectT1_autoEstimateAlveusML.app
That should be in /Applications/freesurfer/7.1.0/bin/
Thank you for any help!
Angela
Hi Angela,
This is a bit odd. It looks like segmentSubjectT1_autoEstimateAlveusML.app exists in the release tar, but doesn’t get installed by the pkg installer. Thanks for pointing this out, we’ll look into it. In the meantime, you can reinstall FS from the tar at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darw... instead.
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Angela Favaro angela.favaro@unipd.it Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Sunday, May 24, 2020 at 3:58 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] hippocampal segmentation freesurfer 7.1.0
External Email - Use Caution Hi all, I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for hippocampal segmentation) that is lacking. How can I obtain it?
The file is a Matlab script:
segmentSubjectT1_autoEstimateAlveusML.app
That should be in /Applications/freesurfer/7.1.0/bin/
Thank you for any help!
Angela
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ok thank you! Can you help me with my question about the longitudinal script? My message is reported below....
Dear Freesurfer experts, I am trying to process a dataset with a longitudinal design.
However, after building the template, at the “recon-all -long” command I got this error:
longmc Done
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
\n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
ERROR:
Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
Angela "Hoopes, Andrew" AHOOPES@mgh.harvard.edu ha scritto:
Hi Angela,
This is a bit odd. It looks like segmentSubjectT1_autoEstimateAlveusML.app exists in the release tar, but doesn’t get installed by the pkg installer. Thanks for pointing this out, we’ll look into it. In the meantime, you can reinstall FS from the tar at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darw... instead.
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Angela Favaro angela.favaro@unipd.it Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Sunday, May 24, 2020 at 3:58 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] hippocampal segmentation freesurfer 7.1.0
External Email - Use CautionHi all, I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for hippocampal segmentation) that is lacking. How can I obtain it?
The file is a Matlab script:
segmentSubjectT1_autoEstimateAlveusML.app
That should be in /Applications/freesurfer/7.1.0/bin/
Thank you for any help!
Angela
-- Angela Favaro Professore di Psichiatria Direttore UOC Psichiatria Azienda Ospedale Università di Padova Direttore Scuola di Specializzazione in Psichiatria Dipartimento di Neuroscienze Padova Neuroscience Center Universita’ di Padova Via Giustiniani, 2 - 35128 Padova, Italy
freesurfer@nmr.mgh.harvard.edu
-
Angela Favaro -
fsbuild -
Hoopes, Andrew