Hi Peter
you need a colon to separate each of the modifiers you are using, not a space. So
freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay=....
cheers Bruce
On Thu, 14 Jan 2016, Myers, Peter wrote:
Hello all,
I am trying to visualize the results of my GLM analysis. Unfortunately, I keep on running into errors.
I run the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1o verlay=lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_thr eshold=4,5 -viewport 3d
When I do that command, I get the error: Unrecognized sub-option flag 'annot_outline'
I tried to remove this from the command, and freeview opens. But then I get an error saying that freeview cannot open the 'lh.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh' "has many more faces than vertices! Probably trying to use a scalar data file as a surface!"
I tried to open the sig.mgh file through the GUI, but then freesurfer completely crashes with the following error: [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 seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[0]PETSC 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 sunshine by myerp Thu Jan 14 11:14:53 2016 [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 (core dumped)
Any help is greatly appreciated!
Thanks, peter
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