Freesurfer

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developer login
by Guillaume Pech 05 Feb '22

05 Feb '22

1 0

Developer Login
by Guillaume Pech 05 Feb '22

05 Feb '22

1 0

Re: [Freesurfer] Updated Mac to Monterey, issues with Freesurfer
by fsbuild 04 Feb '22

04 Feb '22

External Email - Use Caution Hello Lisa, Are you running the 7.2.0 release, e.g. as installed by the package installer,  https://secure-web.cisco.com/1WrA-NZx66e293R6KJNdyTGSNLLRCP3adzgCpi5RDIvdwv… ?? After the package install, it will be listed in the Finder as /Applications/freesurfer/7.2.0 - R. On Feb 4, 2022, at 17:15, Taylor, Lisa <ltaylor2(a)hs.uci.edu> wrote:        External Email - Use Caution        Hi there, Not exactly sure if you'll be able to help but I am a bit stumped. I recently updated my MAC os to the new monterey update. I now get these error messages when trying to use Freesurfer, or even freeview:viewfreesurfer PATH/MRI/Freesurfer 2022-02-04 09:50:46.970 Freeview[476:2201959] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0viewfreesurfer:4: command not found: [0]PETSC[\w]$ freeview2022-02-04 09:51:20.263 Freeview[777:2204165] *** 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://secure-web.cisco.com/1ms4uWzVnFfUyjwx3Q4TOmbOyaHG14QccfYH-M…: or try http://secure-web.cisco.com/1NcuTEBWMPSP0hSarumWN6v5_tx3tAZjQ4BCPG… 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 Taylor-Desktop.local by taylorl Fri Feb  4 09:51:18 2022[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 0I am not exactly tech savvy to understand how I can go about this to remedy it. Any advice?Thank you so much..LisaThis message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Updated Mac to Monterey, issues with Freesurfer
by Taylor, Lisa 04 Feb '22

04 Feb '22

External Email - Use Caution Hi there, Not exactly sure if you'll be able to help but I am a bit stumped. I recently updated my MAC os to the new monterey update. I now get these error messages when trying to use Freesurfer, or even freeview: viewfreesurfer PATH/MRI/Freesurfer 2022-02-04 09:50:46.970 Freeview[476:2201959] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 viewfreesurfer:4: command not found: [0]PETSC [\w]$ freeview 2022-02-04 09:51:20.263 Freeview[777:2204165] *** 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://secure-web.cisco.com/1EG_EG7NKVy2YlczWKlaltWyiZxVvICvRft1yFkkckKjOYb… ERROR: or try http://secure-web.cisco.com/1GqQtB0MZCxTV0bZHhEXv3QNy3VG7-5YvXgfSDW1Lq0ByRH… 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 Taylor-Desktop.local by taylorl Fri Feb 4 09:51:18 2022 [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 I am not exactly tech savvy to understand how I can go about this to remedy it. Any advice? Thank you so much. Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Question glm analysis
by Laura Willers de Souza 04 Feb '22

04 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki https://secure-web.cisco.com/1OE5gTnSPStX6C1rqwHBKIDpqIcnp_2ymvTKb8n7oDB8Ix… In a previous analysis (https://secure-web.cisco.com/1I4SmLAoporSfSSXp8cqB6-whkM3uuzSOJ6T9fT_OfoVtM…) Dr Douglas had told me that before any analysis I should test whether the interaction is significant or not. I would like to know if this also applies to this case, the interaction being tested by contrast number 7 of the wiki. Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Re: [Freesurfer] Maps completely painted in freeview
by Laura Willers de Souza 04 Feb '22

04 Feb '22

External Email - Use Caution Sorry, I wrote it wrong! It was intercept contrast. Thanks so much for the explanation! Best, Laura.

1 0

Re: [Freesurfer] mri_normalize error MP2RAGE
by Dr. Cornelius Kronlage 04 Feb '22

04 Feb '22

External Email - Use Caution > Can you send the recon-all.log file? Here you go, two examples. Thank you! Best Cornelius

1 0

mri_concat error
by Mateus Aranha 04 Feb '22

04 Feb '22

External Email - Use Caution Dear all, I'm constantly getting the following error and I have no idea where the problem is... [image: image.png] Thanks for your help, Mateus

2 2

Maps completely painted in freeview
by Laura Willers de Souza 04 Feb '22

04 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I am performing an analysis of the relationship between cortical thickness and cortisol, following exactly what is on the wiki https://secure-web.cisco.com/1FfPt4RYxp7QhaPPGponDxJJ_3LvYIPwa_msm03IO6Q5XZ… However, the uncorrected significance map for the interaction contrast is turning completely yellow, for both hemispheres. After correcting for multiple comparisons, the result is a whole-brain cluster, for both hemispheres too. The pcc.mgh map is also fully painted. But the maps for the slope contrast are correct. I am sending the fsgd file, the matrix files, the commands that I run and what appears on the command screen after running the commands to open the significance and pcc.mgh maps in freeview. (I'm not sending example images because my email has already been denied for being too big). Was this supposed to happen? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Unsure About Longitudinal & GLM Tutorials
by Edwards, Vincent 04 Feb '22

04 Feb '22

External Email - Use Caution Good morning Freesurfer Team! I would like to use GLM on my longitudinal study to measure change between two time points. I followed the longitudinal tutorial, and to my understanding, I would move on to the general glm tutorial next. The longitudinal tutorial says that "you can compare groups similar to a cross sectional analysis", but when we run stats on our significant clusters our results look "odd". I may have misunderstood the tutorial, but I plugged the longitudinal timepoints into my fsgd file like this: Input Subject1_TP1 subject 57 0.93 Input Subject1_TP2 subject 57 0.93 Input Subject2_TP1 subject 64 1.22 Input Subject2_TP2 subject 57 1.22 I'm not sure if what we ran is actually finding change between timepoints in our subjects. We happened across a glm paired-analysis tutorial. Should we re-run our data through that instead? The longitudinal tutorial only referenced the regular glm tutorial, so I want to make sure that we are following the correct steps - perhaps there is something I did wrong with my fsgd file? The paired-analysis tutorial seems like it may be appropriate, but I was hoping you could clear up our confusion before we move forward. Thank you, Vince

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