Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Error opening Freeview
by Zeng,Victor (BIDMC - Psychiatry) 01 Jul '19

01 Jul '19

?Hi all, I'm having issues opening Freeview (The most recent version): it loads .mgz and labels correctly, but then after 5 seconds it shuts off, giving off this error: qt_xcb_createCursorXRender: query_pict_formats failed [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 linux-gnu named beta by nick Mon Jul 1 16:25:24 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 Segmentation fault ? I was wondering if there's anything I can do to debug, or whether it's just a lack of computer capacity on our end. Best, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

LME - Monte Carlo
by tom parker 01 Jul '19

01 Jul '19

External Email - Use Caution Dear FreeSurfers, I was reading the wiki documents about how to run LME analyses in FreeSurfer. I found that one of the disadvantages is that, at the moment, it only allows FDR corrections to be applied for multiple comparisons. I have 2 patient groups that show cortical thinning compared to controls at baseline when I correct with Monte Carlo but nothing survives with FDR. Now, I would like to see if these cortical thinning patterns change over time so I thought I should keep things consistent and use Monte Carlo for the longitudinal analysis as well. Is there any way of using Monte Carlo for LME? I read some suggestions in emails that were sent 2 years ago but I was wondering if there are any updates or if there is a guide with recommended steps? Thank you so much!

1 0

Citing the development version for use of hippocampal/amygdala sub-field segmentation
by Daniel Callow 01 Jul '19

01 Jul '19

External Email - Use Caution Hello, I used the longitudinal HippocampalSubfieldsAndNucleiOfAmygdala <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…> pipeline to create subject-specific hippocampal ROI's for a paper I am preparing for submission. I would like to know what the best way to cite this technique is. This is what I currently have in my methods section. Subjects T1-weighted anatomical images were processed with the FreeSurfer image analysis suite (http://surfer.nmr.mgh.harvard.edu/, version 6.0) and Automated hippocampal subfield segmentation was performed for each subjects T1 weighted image using the Freesurfer longitudinal hippocampal subfield segmentation program(Iglesias et al., 2015, 2016). Do I need to cite my use of the development version? And if so how is the best way to go about doing this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

1 0

Surfaces with different numbers of vertices.
by Nillo, Ryan Michael R 01 Jul '19

01 Jul '19

Hello Freesurfer users/developers, I have surface with ~73,400 vertices generated from the Freesurfer version 6 fsaverage brain, left hemisphere. I have a surface map that was created by mapping a volume to the fsaverage white surface. Is there a way to map the surface map to the new surface with less vertices? Is there a way to map values from the 73,000 vertices-map to the standard fsaverage pal surface? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

3 8

Re: [Freesurfer] Question about OptSeq
by Greve, Douglas N.,Ph.D. 01 Jul '19

01 Jul '19

No, there is not. optseq assumes you will be doing an FIR analysis (=finite impulse response = not assuming a shape to the hemodynamic response). In this analysis, this must be the relationship. If you assume a shape, then this relationship is not necessary. In your case, you can set the dPSD=1. On 7/1/2019 7:19 AM, Davide Nardo wrote: External Email - Use Caution Dear Prof Greve, I hope you don’t mind if I ask you a question about OptSeq. It looks like a constraint in using OptSeq is that any event duration must be an integer multiple of the dPSD, which in turn needs to be an integer multiple of the TR, and seemingly there is no exception to this rule. I am in a situation in which my TR = 2 sec, and my event duration = 3 sec, therefore I get an error message when running OptSeq. However, I am puzzled by this, as in my experience with fMRI an event duration does not necessarily need to be a multiple of the TR… Is there any way I can circumvent this requirement in OptSeq? Best. Davide Nardo -- Davide Nardo, PhD MRC Cognition and Brain Sciences Unit University of Cambridge 15 Chaucer Road Cambridge, CB2 7EF Davide.Nardo(a)mrc-cbu.cam.ac.uk<mailto:Davide.Nardo@mrc-cbu.cam.ac.uk>

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Freesurfer July 2019