Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30056 discussions

Re: [Freesurfer] freesurfer as module
by fsbuild 02 Jul '24

02 Jul '24

External Email - Use Caution  My understanding is that it is up to the sysadmins who run a cluster to choose how to present and configure the apps they host whether it be thru modules, spack, or other tools.  We don't track how cluster admins do that, but you could ask the helpdesk for the cluster you are going to use (which presumably lists there is some version of freesurfer already available on the cluster).  Most have online documentation stating how to run their apps. I have used Freesurfer in the past on the SDSC cluster, and according to their web pages, they do use modules,https://www.sdsc.edu/support/user_guides/expanse.html#software - R. On 7/1/24 14:55, Dong, Yilei (yid025(a)health.ucsd.edu) wrote Hi Freesurfer Developers,  If Freesurfer is available as a module on a computer cluster, is it still necessary to source/configure the freesurfer module in a .bashrc script on Linux?  Sincerely, Yilei  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Freeview cannot be opened (MacOS)
by fsbuild 02 Jul '24

02 Jul '24

External Email - Use Caution   If you prefer to run the last stable release (7.4.1), then I suggest downloading and installing the Intel binary package installer, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-mac…  To bypass some security prompts, right click on the package file and then choose "open will default ..." You should check the path, but I think you would set things up in the (bash) shell as, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1... source the environment setup script ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh If you don't mind running the latest development build (which can be unstable), then you can try the native arm64 binary package installer via the link, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS… Install the same way via right click as listed above.  Then check the path, e.g, $ export FREESURFER_HOME=/Applications/freesurfer/dev... source the environment setup script  ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Assuming you have your license file setup, e.g., to be read via FS_LICENSE environment variable with license.txt under your home directory, $ export FS_LICENSE=$HOME/license.txt - then it should work to run freeview.  I would first try running freeview from the shell command line w/o any arguments to see if it opens an empty window.   $ freeview Then exit and try it again with a known to be good volume, $ freevivew $SUBJECTS_DIR/bert/mri/brain.mgz - R. On 7/1/24 13:42, Melih Keskin (keskinmelih07(a)gmail.com) wrote:         External Email - Use Caution         Hi, I am trying to open Freeview using my M1 Macbook (Monterey version 12.5). I am posting the error it gives me below. I followed the steps from the below thread but none of the solutions worked (mainly changing the privacy settings and getting a new Freesurfer license). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/… Is there a solution to this problem as of 2024? Thank you in advance,Melih 2024-07-01 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead.  [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run  [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a darwin12. named Melihs-MacBook-Pro.local by keskin Mon Jul  1 20:41:01 2024 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Calculating intensity of Individual voxel
by ERNEST KISSI 02 Jul '24

02 Jul '24

External Email - Use Caution Hi, freesurfer team Is there a way to calculate the intensity of a voxel.Let say, I have a voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be done in freesurfer?

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freesurfer as module
by Dong, Yilei 01 Jul '24

01 Jul '24

External Email - Use Caution Hi Freesurfer Developers, If Freesurfer is available as a module on a computer cluster, is it still necessary to source/configure the freesurfer module in a .bashrc script on Linux? Sincerely, Yilei

1 0

Freeview cannot be opened (MacOS)
by Melih Keskin 01 Jul '24

01 Jul '24

External Email - Use Caution Hi, I am trying to open Freeview using my M1 Macbook (Monterey version 12.5). I am posting the error it gives me below. I followed the steps from the below thread but none of the solutions worked (mainly changing the privacy settings and getting a new Freesurfer license). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70979.html Is there a solution to this problem as of 2024? Thank you in advance, Melih 2024-07-01 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a darwin12. named Melihs-MacBook-Pro.local by keskin Mon Jul 1 20:41:01 2024 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

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recon-all is shutting down? because of flair?
by egemen gok 30 Jun '24

30 Jun '24

External Email - Use Caution *Hello Freesurfer Developers* recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours) and fyi = I used flair image because there was no T1 image of the patient [image: image.png] and this is the log file (recon-all.log) = [image: image.png]

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Can find "mri_WMHsynthseg" command in freesurfer 7.4.1
by Byripudi Naveen Kumar ed20d402 28 Jun '24

28 Jun '24

External Email - Use Caution Dear freesurfer experts, I was trying to use synthseg for segmenting and parcellating a heterogeneous brain with lesions. It is advised in the freesurfer synthseg webpage to use mri_WMHsynthseg command for these cases. How ever when I tried to run the command, it shows that command not found. I checked mri_synsthseg command works. What shall I do to resolve this? Is there a way to install the mri_WMHsynthseg or is it part of some existing commands? Regards, Naveen Kumar

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Inquiry about alpha inflation in multiple comparison
by Emma Harper 28 Jun '24

28 Jun '24

External Email - Use Caution Dear Freesufer teams, Does anyone have any recommendations to correct for alpha inflation when doing the multiple comparisons in freesurfer? We are trying to avoid using the Bonferroni Correction so any recommendations for ways beside that would be greatly appreciated. Thanks, Emma Harper

2 1

FreeSurfer atlases
by Savoia, Alice (Stud. FPN) 28 Jun '24

28 Jun '24

External Email - Use Caution Hello, I am looking for a freesufer standard atlas for hippocampal subfields (to be used for a DTI pipeline in FSL) but I cannot find it in fsaversage/label. Does anyone have any suggestion? Thank for the help, Alice

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Error saying cannot find my file for recon-all
by Lydia Luck 28 Jun '24

28 Jun '24

External Email - Use Caution Hello- I am trying to do recon-all on my brain MRI and I’ve rewritten it so many times I have absolutely no clue what is going wrong. Ultimately, the main error message I’m getting is that my file is not found. I’ve tried typing out the complete path, made multiple different folders, renamed the file and the folders, changed the file type, changed the location of the folder, exited terminal and tried again, switched to the other user on the computer (got the same error) even restarted my computer, etc. Kind of at a loss at this point. I am using a Mac with an M1 chip and the 7.4.1 version This is my current line of commands: export FREESURFER_HOME=/Applications/freesurfer/7.4.1 source $FREESURFER_HOME/SetUpFreeSurfer.sh export FS_LICENSE=/opt/freesurfer/license.txt export SUBJECTS_DIR=$Users/lydialuck/3DBRAIN recon-all -s lydiasbrain -i $Users/lydialuck/3DBRAIN/struct.nii.gz -parallel -all And then getting this back: ERROR: cannot find /lydialuck/3DBRAIN/struct.nii.gz Darwin Blazes-MBP.lan 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64 recon-all -s lydiasbrain exited with ERRORS at Thu Jun 27 01:13:56 EDT 2024 If you could help me figure this out that would be great; I’ve probably spent well over 6 hours now trying different things. Thanks so much, Lydia

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