: Stephanie N. DeCross sdecr...@mgh.harvard.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Cc: Douglas N Greve gr...@nmr.mgh.harvard.edu
Sent: Wednesday, November 5, 2014 10:33:54 AM
Subject: [Freesurfer] Freeview-stable4 error?
Hi,
I'm trying to look at 2 connectivity files (saved
I recently downloaded and installed
freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz .
I had been running this version previously but had to reload everything due to
a disk crash.
recon-all -all goes to completion with no errors.
freeview starts up fine but fails on loading a volume file
you can try downloading our nightly 'dev' build of freeview, from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
or here's a quicker way (this is a one-line command... wget file):
wget
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin
There is no direct way. But you can try this workaround:
Write all the screenshot command in a text file, line by line like this:
-v brain.nii
-viewport sagittal -slice 80 127 127 -ss sag1 -noquit
-viewport sagittal -slice 127 127 127 -ss sag2 -noquit
…
Then run this command:
freeview -cmd
Dear FreeSurfer experts,
I understand that
freeview -v brain.nii.gz -ss screenshot
takes the screenshots and quits the freeview.
Regarding this, I have the following two questions.
(1) Is it possible to suppress the redundant GUI flashing?
It is really a pain when many images are
What date type is your volume? Is it uchar? If so, a value of 570 would
overflow.
Ruopeng
On 07/20/2014 12:25 PM, Tracy Riggins wrote:
Hello Freesurfer experts
I am trying to edit an aseg file. I want to set my brush value to a
value that does not exist in the default lookup table (e.g,.
Hello Freesurfer experts
I am trying to edit an aseg file. I want to set my brush value to a value that
does not exist in the default lookup table (e.g,. 570). So, I edited the
lookup table, saved this , and loaded it in freeview. My new label and brush
value is now visible. However when I
Hi All,
I was hoping that someone might be able to help me.
When I load a surface into freeview (e.g.
/Applications/freesurfer/subjects/fsaverage/surf/lh.inflated), I get an error
in my terminal:
Did not find any volume geometry information in the surface
When I go on to load in my multiple
Hi Derek
this means you don't have file system permission to save the control
point file where you are trying to. Check the subject directory and see if
you have write permission. If not, you will need to talk to your sys admin
to get it fixed
Bruce
On Thu, 5 Jun 2014, Andrews, Derek
Hi all,
Two questions:
First, does Freeview currently support flatmaps, or -patch support still in
development?
Second, I notice some different behavior between tksurfer and freeview
*vis-a-vis
*surface overlays. In tksurfer, we were able to plot volume overlays to
surfaces by specifying a
During the Spring Freesurfer workshop the newest version of Freeview was
used as the primary viewing tool. Are there compatibility issues with
using the newest version of Freeview while running analyses in an older
version of Freesurfer (v5.1.0)? That is, if you run recon-all through
v5.1.0, can
You can use the new version of freeview with older versions of FS.
doug
On 05/13/2014 03:10 PM, Sarah Blankenship wrote:
During the Spring Freesurfer workshop the newest version of Freeview
was used as the primary viewing tool. Are there compatibility issues
with using the newest version of
Hello-
We’re having a problem with our Freesurfer 5.3 install: freeview exits with a
Segmentation fault. No windows open, and there is no other other output.
strohm::funcserv1:=freeview
Segmentation fault
All I have been able to find is that it appears to be making an
Hello All,
Any idea why freeview fails to open? Below I have included the terminal
output.
I have checked my quota and I have plenty of available memory. I also
tried running the 2 options (-start_in_debugger and
-on_error_attach_debugger), but these were not recognized. I was next
going to
Have you tried dev version?
On May 6, 2014, at 10:15 AM, jaco...@nmr.mgh.harvard.edu
jaco...@nmr.mgh.harvard.edu wrote:
Hello All,
Any idea why freeview fails to open? Below I have included the terminal
output.
I have checked my quota and I have plenty of available memory. I also
tried
I have not tried dev version. Can you please let me know how I can load that?
Have you tried dev version?
On May 6, 2014, at 10:15 AM, jaco...@nmr.mgh.harvard.edu
jaco...@nmr.mgh.harvard.edu wrote:
Hello All,
Any idea why freeview fails to open? Below I have included the terminal
output.
Just run:
source /usr/local/freesurfer/nmr-dev-env
On May 6, 2014, at 10:34 AM, jaco...@nmr.mgh.harvard.edu
jaco...@nmr.mgh.harvard.edu wrote:
I have not tried dev version. Can you please let me know how I can load that?
Have you tried dev version?
On May 6, 2014, at 10:15 AM,
Thank you for the source details for dev. I just tried running freeview
under the dev environment and I still received the same error message.
Any other ideas on what may be going on?
Thank you!
Just run:
source /usr/local/freesurfer/nmr-dev-env
On May 6, 2014, at 10:34 AM,
Hi Freesurfer experts,
I'm trying to view aparc.annot on a fsaverage_sym surface.
I can load aparc.a2009a.annot with
freeview -f
$SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.a2009s.annot
but attempting
freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot
results in
It appears to have the same issue on Linux as well. Thanks for the feedback. We
will look into it.
Ruopeng
On Apr 9, 2014, at 5:53 PM, Peggy Skelly peggy.ske...@gmail.com wrote:
Hi Freesurfer experts,
I'm trying to view aparc.annot on a fsaverage_sym surface.
I can load
Hi Jeff
if you send us the .csv file we will see if we can replicate and fix
cheers
Bruce
On Thu,
13 Mar 2014, Jeff Stevenson wrote:
hi freesurfer folks, just had a nasty bug crash my whole mac workstation.
yikes! i loaded lh and rh pial surfaces into freeview and went to assign
annotation
This actually happens on any random non-annotation file. I'll fix it.
Ruopeng
On 03/14/2014 08:25 AM, Bruce Fischl wrote:
Hi Jeff
if you send us the .csv file we will see if we can replicate and fix
cheers
Bruce
On Thu,
13 Mar 2014, Jeff Stevenson wrote:
hi freesurfer folks, just had a
ok, thanks
On Fri, 14 Mar 2014, Ruopeng Wang wrote:
This actually happens on any random non-annotation file. I'll fix it.
Ruopeng
On 03/14/2014 08:25 AM, Bruce Fischl wrote:
Hi Jeff
if you send us the .csv file we will see if we can replicate and fix
cheers
Bruce
On Thu,
13 Mar
hi freesurfer folks, just had a nasty bug crash my whole mac workstation.
yikes! i loaded lh and rh pial surfaces into freeview and went to assign
annotation files to each and when i did i inadvertantly (aka randomly) selected
the wrong file in labels dir- a .csv file i believe - instead of
Hi,
I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the
installation was successful and the paths are set correctly. However, my xterm
crashes when I try to launch freeview. Strangely, the program works as expected
when launched remotely via NX. Has anyone encountered this
My apologies, I meant the X server crashes, not the xterm.
Thanks.
- Archana
-Original Message-
From: Venkataraman, Archana
Sent: Monday, March 3, 2014 1:19 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Freeview crashes xterm
Hi,
I am running freesurfer on a RedHat v6.5
Hi all,
My freeview is not working.
//=//
saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeview
freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file
-WorkStation-T3500:/usr/local/freesurfer$ freeview
freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer
quotes)
on the command line?
-Zeke
On 02/10/2014 05:17 AM, Saurabh Thakur wrote:
Hi all,
My freeview is not working.
//=//
saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$
freeview
freeview.bin: error
Hi Freesurfer experts,
I got to know about freeview.
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsag/FreeviewQuickStart
and went to test it
but getting error :
*saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$
freeviewfreeview.bin: error
Can you post a screenshot?
Ruopeng
On 01/30/2014 12:58 PM, Markus Gschwind wrote:
Dear Experts,
I have installed Freesurfer 5.3 under ubuntu 12.04.
It is running fine except for Freeview which is causing heavy graphic
trouble (thousands of colored squares in the black fields where the
Dear Experts,
I have installed Freesurfer 5.3 under ubuntu 12.04.
It is running fine except for Freeview which is causing heavy graphic
trouble (thousands of colored squares in the black fields where the brains
should be displayed.
Tksurfer is working fine.
Glxgears is showing the rotating
” in FreeView.
-
Date: Mon, 27 Jan 2014 13:31:54 -0500
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freeview Save and Go-to Point Issue
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 52e6a61a.2090...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO
Hi,
I am experiencing an issue where I try to save a point in an inflated brain
view and go to the saved point on my brainmask/wm volume and the point is
jumping to a space off of the brain. This happens consistently. Am I doing
something wrong or is this a bug?
Thank you,
Alexander
Hi Alexander
do you see any error messages in the terminal window where you started
tksurfer?
Bruce
On Mon, 27 Jan 2014, Denker,
Alexander (NIH/NIMH) [F] wrote:
Hi,
I am experiencing an issue where I try to save a point in an inflated brain
view and go to the saved point on my
I was strictly using the freeview GUI and not tksurfer so I didn¹t notice
any error messages.
Alexander
On 1/27/14, 12:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Alexander
do you see any error messages in the terminal window where you started
tksurfer?
Bruce
On Mon, 27 Jan
Would it be possible to share the data that shows this issue? Or does it
happen to any volume you are viewing with freeview?
Ruopeng
On 01/27/2014 12:47 PM, Denker, Alexander (NIH/NIMH) [F] wrote:
I was strictly using the freeview GUI and not tksurfer so I didn¹t notice
any error messages.
It seems to be happening with all of our volumes.
On 1/27/14, 1:23 PM, Ruopeng Wang rpw...@nmr.mgh.harvard.edu wrote:
Would it be possible to share the data that shows this issue? Or does it
happen to any volume you are viewing with freeview?
Ruopeng
On 01/27/2014 12:47 PM, Denker,
Dear doug, bruce and others,
Previously I could not view
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
Dear Ruopeng,
Thanks for your help, Ruopeng.I learned the groupanalysis by manu
ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this
command on your tutorial data (buckner data). Would you please tell me where my
hardware setup is inappropriate?
Thanks.
All the best.
Dear Ruopeng,
Thanks for your help, Ruopeng.I learned the groupanalysis by manu
ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this
command on your tutorial data (buckner data). Would you please tell me where my
hardware setup is inappropriate?
Thanks.
All the best.
Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the
nvidia drivers completely. Then I tried to run this command:
freeview -f
Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and
setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz,
and I setup the nvidia drivers completely. Then I tried to run this
command:
freeview -f
Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the
nvidia drivers completely. Then I tried to run this command:
freeview -f
Hi Alan
yes, this one:
https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf
although it is based on the CMA manual definitions
cheers
Bruce
On
Fri, 6 Dec 2013, Alan Francis wrote:
Thanks Louis and Bruce. One more question: Is there any paper that outlines
the boundaries
Thanks Bruce.
On Fri, Dec 6, 2013 at 2:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Alan
yes, this one:
https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf
although it is based on the CMA manual definitions
cheers
Bruce
On Fri, 6 Dec 2013, Alan Francis
Hi Bruce et al,
Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a
brain in Freeview?
thanks,
Alan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
Hi Alan,
You can use mri_binarize to pull it out of the aseg.mgz. FYI: Once loaded
into freeview you can also generate an isosurface for the hippocampus
label in the 3D view.
-Louis
On Thu, 5 Dec 2013, Alan Francis wrote:
Hi Bruce et al,
Is it possible to load just the Hippocampal
Thanks, Bruce...
Do you know if you also have to specify the full path for the location
of *input
**and **output* files in mris_preproc, mri_surf2surf, and mri_glmfit?
By default, when I ran the above programs, my output files were placed in
my computers home directory and not my freesurfer home
you don't need to supply the full path to the inputs of mris_preproc,
but you must for the output of mris_preproc as well as the input and
output of surf2surf and glmfit
On 11/28/13 1:25 PM, Laura Taylor wrote:
Thanks, Bruce...
Do you know if you also have to specify the full path for
Hi,
I previously installed set-up and have successfully used freesurfer to run
recon-all and visualize my results in tkmedit and tksurfer. However when I
went to analyze my data and also view it in freeview I have run into a
problem with what my home directory is considered for these
Hi Laura
freeview by default doesn't use any of the environment variables. You
need to give it the full path to the data you are trying to visualize. It
included your home dir in the path probably because that was your pwd.
cheers
Bruce
On
Wed, 27 Nov 2013, Laura Taylor wrote:
Hi,
I
Hi all,
I recently updated to FreeSurfer version 5.3.0, and I am now having
problems with freeview that I didn't have on the older versions. When I go
to Surfaces and Load Labels, it only shows one label at a time.
Previously, I could add several labels and all would appear on the Figure.
Does
Hi Lindsay,
I think there was no such option to display multiple surface labels at
once even in the old version. However, we will add it in the future.
Best,
Ruopeng
On 10/28/2013 01:48 PM, Lindsay Squeglia wrote:
Hi all,
I recently updated to FreeSurfer version 5.3.0, and I am now having
Was that from freeview or tksurfer?
On 10/28/2013 02:06 PM, Lindsay Squeglia wrote:
Hi Ruopeng,
Thanks for your response! I used to do it all the time in the previous
versions of FreeSurfer (see attached). I am not sure why the new
version is different.
Thanks!
Lindsay
On Mon, Oct 28,
It was definitely from freeview. These are the notes I wrote for creating
figures previously, and I didn't have a problem:
**Type freeview in command line in file where Freesurfer fsaverage brain
is, will open file, go to File-- Load Surface --fsaverage--surf. Choose
lh.pial; then do again for
Hi, When trying freeview command (see below) from the “Testing your
freesurfer installation” page using my own data, freesurfer opened, but I
am concerned about the “invalid drawable” lines. The message happened when
I ran this command on the bert data too. What does invalid drawable mean?
You can just ignore this warning message on Mac.
Best,
Ruopeng
On Oct 23, 2013, at 8:52 PM, Elissa McIntosh mcintosh.eli...@gmail.com wrote:
Hi, When trying freeview command (see below) from the “Testing your
freesurfer installation” page using my own data, freesurfer opened, but I am
Hi Kambiz,
It would still be very helpful if you could send us the volume and the surface
files so that we can investigate.
Thanks,
Ruopeng
On Oct 16, 2013, at 4:10 PM, Kambiz Tavabi ktav...@uw.edu wrote:
Hi Ruopeng,
Sorry for the confusion in my initial post. The screen capture is actually
Would it be possible to send us the command line and the files that produces
the screenshot?
Thanks,
Ruopeng
On Oct 16, 2013, at 2:28 PM, Kambiz Tavabi ktav...@uw.edu wrote:
I would like to inspect the results of my surface boundary on the volume as
per the approach in tkmedit. However in
Hi Ruopeng,
Sorry for the confusion in my initial post. The screen capture is actually
a grab from one of the viewing windows in FREEVIEW; so I am actually not
doing anything on the command line with tkmedit. In freeview, I am loading
the original T1 volume and then loading the skin, outer skull,
Simply to make sure,
1) Is there no way that one can edit two volumes simultaneously similarly to
tkmedits aux+main volume brush?
2) When editing voxels in freeview, is there anyway to have the cursor behave
the same way it does in navigation mode. That is, I'd like to be able to see
exactly
Hi Jon,
1) No, there is no way to do that in freeview.
2) In Editing mode, you can use shift+ctrl+Left mouse button to move the
cursor.
Ruopeng
On 10/01/2013 12:50 PM, Jonathan Holt wrote:
Simply to make sure,
1) Is there no way that one can edit two volumes simultaneously similarly to
Thank you Zeke. I am trying to run freeview remotely and display locally on
a machine (using Xming). The computer from which I am connecting can
successfully run freeview from a different ubuntu 13 machine (one which
does not have a cuda graphics card / cuda drivers). When I run glxgears
(required
Hi,
When I try to run freeview on my ubuntu 13 machine, running the nvidia 5.0
cuda drivers, I get the following errors:
Xlib: extension NV-GLX missing on display localhost:10.0.
Xlib: extension NV-GLX missing on display localhost:10.0.
Xlib: extension NV-GLX missing on display
Hello Sal,
Are your trying to run freeview remotely and display locally machine? If
you type 'glxgears' at the command line does a window popup displaying
spinning gears?
-Zeke
On 08/16/2013 05:55 AM, Salil Soman wrote:
Hi,
When I try to run freeview on my ubuntu 13 machine, running the
Hi there,
Occassionally when using the save volume function from the gui to save
edits made to the wm.mgz, freeview crashes (see command line error report
below) and the wm.mgz being deleted from subject's 'mri' directory (the
temp wm.mgz~ is still present...but all edits are lost). I am running
Hi Jason
any chance you can figure out how to replicate this reliably? If so, we
can track it down. Otherwise it's going to be hard
thanks
Bruce
On Mon, 22 Jul 2013,
Jason Tourville wrote:
Hi there,Occassionally when using the save volume function from the gui to
save edits made to the
Hi Jason,
Yes, although I think it's only an option in freeview from the 5.2/5.3
Freesurfer releases.
-Louis
On Thu, 18 Jul 2013, Jason Tourville wrote:
Hi there,The tksurfer/tkmedit combo allowed one to select and save a point on
the
inflated surface and then go to that point in the
Hi there,
The tksurfer/tkmedit combo allowed one to select and save a point on the
inflated surface and then go to that point in the volume. Does freeview
have a similar capability?
Thanks,
Jason
--
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and
Hi Jason
yes, there should be a similar button on the interface, or you can just
copy the vertex # and paste it into the freeview interface.
cheers
Bruce
On Thu, 18 Jul
2013, Jason Tourville wrote:
Hi there,The tksurfer/tkmedit combo allowed one to select and save a point
on the inflated
Hi list,
is it possible to create a ROI in an inflated surface within freeview or do
I have to use tksurfer?
It seems that I only can edit volume files.
After exploratory mri_glmfit, I want to outline a ROI in fsaverage inflated
surface and afterwards create a label to obtain CT averages per
Dear Koen,
Freeview returns 8 lines of the error message invalid drawable whenever
executed. The messages are as follows
2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.944 Freeview[1937:303] invalid
Hi Freesurfer experts,
I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the
reposition tool now has a GUI and it works!
Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012
that the pipeline for the reposition surface tool was not yet implemented
and you
There is a screenshot option -ss from the command-line. Run 'freeview -h' will
show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com
wrote:
Hi list,
is it possible to automate Freeview automation from the command line?
I
Ender asked me to forward you this:
I had to automate freeview recently.
Freeview can be used via command line.
For options please write
freeview -h
in the console / terminal.
An example command that produces a surface and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth
Thanks!
I can visualize the 3D renders of interest with different colors, but from
freeview -h I couldn't get the following: is it possible to automatize
the File Save movie frames option?
Thanks again!
Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu
Sure.
I couldn't find that option neither.
What I did was to semi-automatize.
I wrote a batch file to call freeview multiple times with different
parameters.
Each time freeview pops up and I save the image/video. During this time
the process in the terminal waits for me.
When I shut that
Thanks Ender,
I am trying to make a command file with multiple commands too in order to
have snapshots from different views.
thanks for the help!
Gari
On Fri, May 31, 2013 at 5:13 PM, Ender Konukoglu end...@nmr.mgh.harvard.edu
wrote:
Sure.
I couldn't find that option neither.
What I did
If you use '-ss' option, freeview will save a screenshot and close
itself. For example:
freeview -v foo.mgz -ss foo.jpg
On 05/31/2013 11:13 AM, Ender Konukoglu wrote:
Sure.
I couldn't find that option neither.
What I did was to semi-automatize.
I wrote a batch file to call freeview multiple
Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf
template in either fsaverage or fsaverage_sym directory.
FYI, I'm using freeview v1.0
if anybody know, please help.
-Glen
$ freeview -f lh.inflated
2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid
On a Mac? You can just ignore those warning messages. Unfortunately we
were unable to remove them.
Ruopeng
On 03/20/2013 04:07 PM, Glen Lee wrote:
Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf
template in either fsaverage or fsaverage_sym
On Sunday, December 02, 2012 23:56:38 Yaniv Kaufman wrote:
Dear Freesurfer experts,
I am trying to display DTI using freeview, however, every time I attempt to
run freeview from the command line (I am using Ubuntu 12.4), I receive the
following error:
freeview.bin: error while
Dear Freesurfer experts,
I am trying to display DTI using freeview, however, every time I attempt to run
freeview from the command line (I am using Ubuntu 12.4), I receive the
following error:
freeview.bin: error while loading shared libraries: libjpeg.so.62:
cannot open shared
Hi, I am trying to use freeview to look at wm/brainmask etc however the
command wont work. The command Im suing is
freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4
wm1_edits_before/mri/brainmask.mgz \
-f wm1_edits_before/surf/lh.white:edgecolor=blue
Hi, Freeview does not look up SUBJECT environment variable. So you will
need to cd into your subject directory before running the command, or
use the full path in the command for every file.
Ruopeng
On 11/7/12 9:50 AM, Catherine Bois wrote:
Hi, I am trying to use freeview to look at
Hi Freesurfers,
I've recently moved onto Ubuntu 12.04. The Freesurfer installation has
required me to download various libraries and create many symbolic links to
have it working. Further more I've had to set the doublebufferflag=1
(whatever that is) in order for tkmedit and freeview to work
Dear Experts:
I have worked my way through Tracula and
things seem to work fine, but when I try to view my tractography
outputs I get the following persistent error using freeview (copied
below).
I am using a Mac OS X 10.6.7.
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Could this
does freeview otherwise appear to be working? that is, does it crash?
the 'invalid drawable' messages can be ignored on the mac.
n.
On Wed, 2012-08-29 at 14:29 -0700, Cat Chong wrote:
Dear Experts:
I have worked my way through Tracula and things seem to work fine, but
when I try to
: Wednesday, August 29, 2012 2:35 PM
Subject: Re: [Freesurfer] freeview tracula error
does freeview otherwise appear to be working? that is, does it crash?
the 'invalid drawable' messages can be ignored on the mac.
n.
On Wed, 2012-08-29 at 14:29 -0700, Cat Chong wrote:
Dear Experts:
I have
Hi list,
I am looking for a complete reference to scriptable commands for Freeview,
comparable to what exists for tksurfer (e.g.
http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference)
Does this exist?
Thanks!
___
Hi Inge,
Freeview does not support tcl scripting. It does have lots of
command-line options that might fit your need. Run 'freeview -h will
display a complete list of the available options.
Best,
Ruopeng
On 6/29/12 7:16 AM, Inge Kasbohm Amlien wrote:
Hi list,
I am looking for a complete
Hi Hiroyuki, can you give us more information? Eg, you click on a given
vertex (col,row,slice), you find the Scanner RAS field in tkmedit, you
go to the same col,row,slice in freeview and it's RAS is x,y,z. There
are several different RAS coordinates, and you'll need to be clear as to
which
Dear Sir,
When I view a brain volume (e.x., orig.mgz) with freeview and tkmedit, RAS
coordinate differs. Why?
Thank you.
Hiroyuki
Notice: This UI Health Care e-mail (including attachments) is covered by the
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Nachricht-
Von: Ruopeng Wang [mailto:rpw...@nmr.mgh.harvard.edu]
Gesendet: Mittwoch, 16. Mai 2012 18:30
An: Focke, Niels
Betreff: Re: AW: [Freesurfer] Freeview chrash
Hi Niels,
Are you using non-English terminals? I think we found the reason. But no fix
yet. The work around is to set your
Dear Ruopeng,
to reproduce the problem with :
MatrixMultiply: m2 is null! and the seg fault.
$source /usr/local/freesurfer/nmr-stable51-env
$cd ~gramfort/cluster/work/data/MNE-sample-data/subjects
$setenv SUBJECTS_DIR $PWD
$freeview -f sample/surf/lh.inflated
if you cannot access this folder
Hi,
I am looking for an option to script freeview as I could tksurfer via TCL.
I checked the command-line options, and there is a -cmd Load freeview
commands from a text file, but I could not find any documentation about the
language/syntax/commands.
Could someone tell me, where can I find
Hi,
a bit connecting to my previous mail:
How can I overlay an FSL activation map onto the surface in FreeView? The
solution working in tksurfer (i.e. overlay) is not working here. I can load
the data as a volume, but then it is not projected to the surface.
Thanks,
Auer, Tibor M.D.
Strange. I could not reproduce the error. Niels, I also tried the
surface file you sent me. It loads fine. My colleague could not
reproduce it on his machine, either.
Alex, since you're in the Martinos center, can you try source the dev
version just to see if the same problem exists?
Thanks,
The text file is just lines of freeview command-line options for
convenience. It cannot include shell commands.
Ruopeng
On 5/3/12 5:47 AM, Auer, Tibor wrote:
Hi,
I am looking for an option to script freeview as I could tksurfer via
TCL.
I checked the command-line options, and there is a
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