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: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Thursday, January 14, 2016 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu
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
Freesurfer@nmr.mgh.harvard.edu
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. If you have received this email
in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
