glad to hear it On Thu, 14 Jan 2016, Myers, Peter wrote: > It's working now! > Thank you everyone for your help. > Some settings in the GUI seemed off for some reason. > ________________________________________ > From: [email protected] > <[email protected]> on behalf of Bruce Fischl > <[email protected]> > Sent: Thursday, January 14, 2016 12:39 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Visualizing GLM analysis error > > can you run mri_info on that file? Is it in fact a surface overlay? > On Thu, > 14 Jan 2016, Myers, Peter wrote: > >> >> Thanks for these comments/suggestions. Still having troubles unfortunately. >> >> >> I ran the command: >> >> freeview >> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.Cog_T >> rial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh:overlay_threshold=4,5 >> -viewport 3d >> >> >> I don't think there are any spaces, only colons as suggested. And I removed >> the 'annot_outline' part as it does not seem to be in my 5.3 version. >> >> >> I still get this error message: >> >> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l >> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open >> file >> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l >> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open >> file >> could not read overlay data >> from/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.Cog_Tr >> ial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh >> mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/l >> h.Cog_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh, -1): could not open >> file >> ^C >> >> as well as a message from freeview that says 'failed to load surface >> overlay' >> >> I've double checked and the sig.mgh file exists in the directory, but for >> some reason, it seems unable to be loaded? >> >> >> Thanks much, >> >> peter >> >> >> ____________________________________________________________________________ >> From: [email protected] >> <[email protected]> on behalf of Douglas Greve >> <[email protected]> >> Sent: Thursday, January 14, 2016 12:06 PM >> To: [email protected] >> Subject: Re: [Freesurfer] Visualizing GLM analysis error >> also, I think that the annot_outline is a version 6 feature. >> >> On 1/14/16 1:01 PM, Bruce Fischl wrote: >> 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: >> orseehttp://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 >> linkedfrom/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 >> >> >> >> >> >> ___________________________________________________________________________ >> _ >> >> >> The materials in this message are private and may >> contain Protected >> Healthcare Information or other information of a >> sensitive nature. If you >> are not the intended recipient, be advised that any >> unauthorized use, >> disclosure, copying or the taking of any action in >> reliance on the contents >> of this information is strictly prohibited. If you >> have received this email >> in error, please immediately notify the sender via >> telephone or return mail. >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> ____________________________________________________________________________ >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. 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