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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_Trial1.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/lh.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/lh.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_Trial1.glmdir/lh-Avg-thickness-Cog_Trial1/sig.mgh
mghRead(/data/jsp/human2/fcMRI/PickettK/Data/FreeSurfer5.3/fsaverage/surf/lh.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
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: 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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