Hi Catherine,
This question might not fit in freesurfer mailing list but I'll answer here
anyway - Unfortunately, for the command-line track_vis, there is no such
option.
Ruopeng
On May 7, 2013, at 9:53 AM, Chu, Catherine,M.D. cc...@partners.org wrote:
Dear Freesurfer/TrackVis experts,
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
and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
Let me know if this helps.
Cheers,
E
On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
There is a screenshot option -ss from the command-line. Run
'freeview -h' will show you all
Would it be possible to send us the volume and control point files?
Thanks,
Ruopeng
On 09/25/2013 02:09 PM, Jonathan Holt wrote:
I've read in the mailing list archives people have had issues with tkmedit
and free view displaying control points differently. For me the first brain
I've loaded
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
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
, 2013 at 12:26 PM, Ruopeng Wang rpw...@nmr.mgh.harvard.edu
wrote:
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
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 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
, 2013 at 11:01 AM, Ruopeng Wang
rpw...@nmr.mgh.harvard.edu mailto:rpw...@nmr.mgh.harvard.edu wrote:
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
Hi Rujing,
Your hardware setup does sound a bit insufficient to run freeview smoothly. But
I don't think that is the reason configure overlay hangs. Would it be
possible to send us the files used in your command?
Best,
Ruopeng
On Dec 31, 2013, at 1:04 AM, rujing cha charuj...@gmail.com
Hi Rujing,
I am able to replicate the issue with 5.3.0 release. The good news is the issue
does not appear in the current dev version (so I think it has been fixed).
Zeke, would it be possible for Rujing to download a copy of the latest freeview
build?
Best,
Ruopeng
On Jan 4, 2014, at 10:40
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.
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
Hi Jon,
The range of color bar is automatically set by the internal color bar
component that is used to display it. There is no option to change it at
this point. I'll take note on that for future update.
Best,
Ruopeng
On 02/10/2014 11:49 AM, Jonathan Holt wrote:
Hi all,
Would someone
Hi Alexander,
Eraser value is used for erasing. Brush value is used for drawing. To
erase, just hold shift key and press left mouse button.
Best,
Ruopeng
On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote:
Hi all,
This is probably a very elementary error in my use of Freeview,
You can load surface-based time course data as a surface overlay, I believe.
But there is no function to view the scatter plot. The time course window is
for volume only.
Ruopeng
On Feb 26, 2014, at 10:13 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
That command definitely will not
I have added support to display surface-based timecourse data in Time
Course window. It should be available in the dev build tomorrow.
Ruopeng
On 02/27/2014 12:17 AM, charujing123 wrote:
Hi doug and Ruopeng,
Thanks doug.
The command you sent did show something on the surface, but the button
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
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
OK. I'll put in license checking.
On 04/11/2014 10:57 AM, Bruce Fischl wrote:
I think we need to distribute it with a license for NIH-accounting
purposes. The license is free and trivial to get so it's not really
much of a hardship
On Fri, 11 Apr 2014, Ruopeng Wang wrote:
I have a stand
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
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,
Hi Lucette,
Are you saying that the label file saved by freeview can not be loaded
by other tools in freesurfer? Can you post the complete commands and
output that did not work?
Best,
Ruopeng
On 05/27/2014 02:03 AM, Lucette Cysique wrote:
Dear Ruopeng and colleagues,
I am interested in
Are you running the dev version of freeview?
Ruopeng
On 06/19/2014 11:27 AM, Bernardoni, Fabio wrote:
Dear all,
trying to follow the freesurfer longitudinal tutorial I encounter the
following problem.
Commands I digit in a new shell:
~tcsh
~source $FREESURFER_HOME/SetUpFreeSurfer.csh
That is correct. timecourse option is only available in dev version. You can
download it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
You may want to make a backup of your current freeview.bin file.
Ruopeng
On Jun 20, 2014, at 3:25 AM, Bernardoni, Fabio
If you are running freeview on a Mac, you can ignore those “Invalid drawable”
messages. Can you post a screenshot of the whole freeview window with the color
bar issue?
Best,
Ruopeng
On Jul 20, 2014, at 11:34 PM, 郝磊 haolei0...@gmail.com wrote:
Dear experts
when I open freeview, it
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,.
Hi Shannon,
If I understand correctly, you are trying to load 2 ROIs on top of a layer of
annotations on surface? Can you show me the freeview command you run? Or did
you do everything on the GUI? BTW, are you using the latest dev build of
freeview or the released one in v5.3? If I remember
Can you try re-run that freeview command again? I remember I saw similar
problem once, but somehow I could not reproduce it when I re-run the
same command. If you can positively reproduce it, would it be possible
to send us all the files that are used in the command?
Best,
Ruopeng
On 6/26/12
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 Michael,
In freeview you can press Page up/down keys to move through slices.
Best,
Ruopeng
On 7/2/12 5:30 AM, Michael Scheel wrote:
Dear FS experts,
I am trying out freeview and am extremely fond of it.
I have one feature request. In tkmedit in navigate mode it was possible
moving
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
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
Are you running the latest release version? Would it be possible to send
us the surface file and the overlay file that crashes?
Best,
Ruopeng
On 6/16/2011 3:34 PM, iac...@nmr.mgh.harvard.edu wrote:
Hi all,
I am trying to overlay a map on a specific subcortical structure (the
caudate).
-I
Hi Maria,
I've tested the files you sent me and were able to replicate the
problem. Will work on it asap. Sorry about the delay.
Ruopeng
On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote:
Hi all,
I haven't had any answer to my post, so I give another try. Hope it
doesn't bother
Hi Maria,
The fix is done and should be available in tomorrow's dev build.
Ruopeng
On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote:
Hi all,
I haven't had any answer to my post, so I give another try. Hope it
doesn't bother you.
I am trying to overlay a map on a specific
If you run:
glxgears
will it crash too?
On 8/7/11 1:39 PM, Hoptman, Matthew wrote:
Hi all,
I've been using Freesurfer for several years. I just upgraded to v.
5.1, but when I try to run freeview it crashes. I am running it on a
64-bit Centos 5.4 server and am accessing the server with
If you run 'glxgears' command, does it get similar error?
Ruopeng
On 9/27/11 8:40 PM, Satrajit Ghosh wrote:
hi,
we are seeing a strange freeview issue at mit and just wanted to check
if anybody else has seen this. we are running natty narwhal (ubuntu
11.04).
details here:
They are standard parameters to linearly map a voxel value (val) into
heat-scale color (c), something like this:
first apply offset:
val = val + offset
then:
if val = min, c = black
if min val mid, c = between black and red
if val = mid, c = red
if mid val max, c = between red and
Does it happen with just that file or with other files as well? Would it
be possible to send us that volume file?
Ruopeng
On 12/08/2011 02:03 PM, Xin Zheng wrote:
Hi,
We are trying to open something using freeview (ie. freeview -v
SubjectID_template/mri/norm.mgz) and would get a
I have no problem loading this file in freeview, in both old and new
versions. Have you used freeview before on the same system? Did it work?
Ruopeng
On 12/08/2011 02:33 PM, Xin Zheng wrote:
Hi Ruopeng,
It seems to be with all files. Attached is one of them.
Thanks!
Xin
On Thu, Dec 8,
Would be hard for us to diagnose if we can't replicate the issue. Is
there any core dump file or some kind of log file that may provide any
hint? From what you described, it seems freeview crashes right when it
is about to render the loaded image. that's about as far as I can guess
now. Is
I should be able to add an option for that. However, JFYI, a better way
to toggle on/off a volume is Alt+V.
Ruopeng
On 12/18/11 9:46 PM, Thomas Yeo wrote:
Hi,
I noticed that when viewing multiple volumes in freeview (5.1.0, snow
leopard), double-clicking on a volume will bring the volume to
You can find some instruction here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide
Ruopeng
On 12/28/11 11:49 AM, Sabin Khadka wrote:
Dear all,
Is there any documentation on doing em edit using freeview.
Thanks,
SK
___
Freesurfer mailing
Unfortunately no. I'll update it in the next release.
Ruopeng
On 3/4/12 9:11 PM, Blazey, Tyler wrote:
Hi,
Is there any way to prevent the NIH color map in Freeview from displaying
values higher than the max as black? I can only seem to find this option for
the Heat color map.
Thanks for
According to freesurfer release notes
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes, Freeview in
version 5.0 does not work on Snow Leopard. Version 5.1 has fixed it.
Ruopeng
On 04/10/2012 04:36 PM, Jeni Chen wrote:
Hi,
I was recently at the FreeSurfer workshop in Boston and learned
Does this happen with every volume you load or just that specific one?
What happens if you change slices? Are you viewing it in the 3D view?
Ruopeng
On 4/13/12 3:34 AM, carlo cotugno wrote:
Dear FreeSurfer experts,
I'm sorry but I have another problem..now when I load a surface
Would it be possible to send us the surface file that crashes freeview?
Ruopeng
On 4/13/12 10:06 AM, carlo cotugno wrote:
I'm a newbie with FreSurfer and Linux. I'm following Longitudinal
Processing-Tutorial. now I have only files of tutorial data set and I
don't have any other file to test.
Hi Richard,
Freeview does not have voxel cloning function between anatomical
volumes. It will be added in the future release. The reference option is
for boundary finding for flood fill and automatic contour finding when
editing labels.
Best,
Ruopeng
On 4/23/12 9:28 PM, Richard Binney
Would it be possible to send us the norm.mgz file and one of the surface
file that causes crash?
Thanks,
Ruopeng
On 4/25/12 6:22 AM, Charlotte Bernard wrote:
Dear Freesurfer users,
I try to visualize my longitudinal data for one subject whit the
command line given in the freesurfer website:
Would it be possible to send us the surface file that caused the crash?
So that we can replicate the problem?
Thanks,
Ruopeng
On 5/2/12 9:35 AM, Focke, Niels wrote:
Dear experts,
I have experienced some problems with freeview. When loading a surface (both
for my locally generated surfaces
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
This is too strange. I logged into the same machine. Both stable and dev
version load the surface file without any problem... We will investigate.
Ruopeng
On 05/03/2012 12:12 PM, Alexandre Gramfort wrote:
Alex, since you're in the Martinos center, can you try source the dev
version just to
What command did you run?
On 01/13/2010 02:43 PM, Gonzalo Rojas wrote:
Hi:
I load orig.mgz using freeview application, but when I try to load
lh.thickness or rh.thickness file, freeview quits unexpectedly... it is
a freeview bug ?...
Sincerely,
: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
El 13-01-2010 16:55, Ruopeng Wang escribió:
What command did you run?
On 01/13/2010 02:43 PM, Gonzalo Rojas wrote:
Hi:
I load orig.mgz using freeview application, but when I try to load
lh.thickness or rh.thickness file, freeview quits
You mean in light box (mosaic) style? No. I will put that on my
features-to-consider list.
Ruopeng
On 3/18/10 10:34 AM, ythomas wrote:
Hi,
is it possible to show all slices (or every N slices) of a volume in
freeview in a particular orientation (e.g. axial or coronal)?
Thanks,
Thomas
Right now you can't. What other color map you'd like?
Ruopeng
On 04/21/2010 11:39 AM, Gonzalo Rojas Costa wrote:
Hi:
Freeview only has grayscale, heat and jet in the color maps for a volume...
How can I specify another color map ?...
Sincerely,
Gonzalo Rojas Costa
Medical Image Processing
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
El 21-04-2010 12:26, Ruopeng Wang escribió:
Right now you can't. What other color map you'd like?
Ruopeng
In freeview if you load the volume first before loading the surface,
they should align.
Ruopeng
On 7/17/10 5:26 AM, Steffen Bollmann wrote:
Thank you so much for your quick response :)
presumably this problem does not occur in tkmedit or freeview?
it works fine in tkmedit, but in freeview
build Aug 11 2009? That's ancient! =-O The latest build shouldn't
have this problem.
Ruopeng
On 7/18/10 3:25 AM, Steffen Bollmann wrote:
the version of freeview I used: 1.0 (internal) build Aug 11 2009
___
Freesurfer mailing list
Do you have a decent graphics card on the box? Also, you may try
updating the graphics card driver to the latest. Do you get the same
problem with dev build?
Ruopeng
On 9/28/10 5:06 PM, B.T. Thomas Yeo wrote:
Hi,
when opening freeview while logged locally on a linux box (at Harvard
NCF),
If you load the data as overlay in freeview, you should be able to
adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.le...@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the
center have this request, so I wanted to
You mean even after you adjust the range of the scale, you still can
only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color
mapping, is that right?
On 11/4/10 11:15 AM, f.le...@donders.ru.nl wrote:
Hi Ruopeng,
Thanks
OK. I'll put that on my list.
On 11/04/2010 11:56 AM, f.le...@donders.ru.nl wrote:
Yup, indeed. There are slight differences in there, but not really clear.
Yup again, a customized color mapping for overlays would fulfill all my
visualization wishes, that would be great!
kind
The complex color options were just placeholders and never implemented.
They will be in the next release (not the one targeted by the end of the
month).
On 11/6/10 7:20 AM, f.le...@donders.ru.nl wrote:
Playing with it some more, I notice the color wheel doesn't work in freeview.
Is that
Hi Alexander,
Would it be possible to send me the volume file and one surface file
that has this shift problem?
Thanks,
Ruopeng
On 11/10/10 9:10 PM, Alexander Hunold wrote:
Dear experts,
I am perplexed how to fix the problem which is shown in the pictures.
The volume is the T1.mgz. The
What does mris_info show on the overlay file?
On 11/14/10 11:08 PM, Gonzalo Rojas Costa wrote:
Hi:
I generated a surface with:
mri_vol2surf --src zstat3.nii.gz --src_type nifti --srcreg ../registro.dat
--hemi lh --projfrac 0.5 --out ./zstat3_lh.w --out_type w
then I tried to load
Unfortunately no. I'll put that on my list and target it for the next
release.
On 11/17/10 9:42 AM, Marco Loggia wrote:
Dear all,
I am trying to use the 3D view in freeview to prepare some figures,
and would like to be able to rotate the volume along one axis only
(e.g., yaw).
Is there a
Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
El 18-11-2010 15:57, Gonzalo Rojas escribió:
Message: 4
Date: Mon, 15 Nov 2010 09:36:17 -0500
From: Ruopeng Wang rpw...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freeview load overlay error
Hi,
The current freeview release does not have that option. However, we've
added the option in our development code. It should be available soon.
Ruopeng
On 1/25/11 3:47 AM, t...@ms36.hinet.net wrote:
Dear Freesurfer experts,
I use freeview to display the cortical thickness. Is it possible
Hi,
I can send you our latest development build if you want to give it a
try. Please let me know what system you are running freesurfer on.
Best,
Ruopeng
On 1/25/11 9:05 AM, Ruopeng Wang wrote:
Hi,
The current freeview release does not have that option. However, we've
added the option
You should be able to pick any location you want to save control point,
when the file dialog shows up.
As to default filename, there is no option to set it in freeview now.
But I believe you only need to manually enter file name the first time
you save it.
Ruopeng
On 2/4/11 6:47 PM, Bruce
Do you mean .trk file? The format is described in detail here:
http://trackvis.org/docs/?subsect=fileformat
Ruopeng
On 2/9/11 10:04 AM, pablo maturana wrote:
Dears expert,
I would like to know how can i get the transformation from trackvis to
a space Freesurfer?.
I have here a link
Would it be possible for you to send me the surface file?
On Jun 3, 2011, at 10:23 AM, Reza Farivar fari...@nmr.mgh.harvard.edu wrote:
Good morning,
I've constructed some monkey surfaces that actually look quite accurate,
but appear dark in Freeview (they render normal in tksurfer). It
Hi,
Annotation option is not available in the stable release version. If you
are able to run the development version, you can load annotation file
from the Surface control panel on the left. Or you can load it from the
command-line like:
freeview -f surface_filename:annot=annotation_filename
Would it be possible to put the volume file somewhere we can download?
It would be much helpful for us to diagnose.
Thanks,
Ruopeng
Mark J. Pearrow wrote:
Hi all,
We are consistently getting segfaults with core dumped from freeview.bin when
trying to open MGZ files that are larger than
You can set background color in freeview from Preferences.
Ruopeng
On Sep 6, 2014, at 9:57 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Angela,
sorry, I'm afraid not, although it is a pretty common request, so maybe
Ruopeng can add it to freeview
Bruce
On Sat, 6 Sep 2014,
You will need to reset FreeView’s settings. Make sure freeview is closed, open
a terminal and run the following command:
defaults delete edu.harvard.mgh.nmr.FreeView
Start freeview again.
Best,
Ruopeng
On Sep 12, 2014, at 4:49 AM, 김영국 engla...@hanmail.net wrote:
Dear,
I lost the
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
You can select a thickness file when loading as generic.
Ruopeng
On Oct 1, 2014, at 10:56 AM, Harms, Michael mha...@wustl.edu wrote:
Hi,
How does one go about loading a thickness map within freeview?
The OutputData_freeview tutorial
Would it be possible to send us your annoy file? Are you using the latest dev
version of freeview or the one with 5.3 release?
Best,
Ruopeng
On Nov 29, 2014, at 4:51 AM, angela.fav...@unipd.it wrote:
Hi all,
I have a problem with freeview and I am not sure about the command line to
be used
Thanks. I can replicate the issue. I’ll look into it.
Best,
Ruopeng
On Nov 30, 2014, at 12:45 PM, angela.fav...@unipd.it wrote:
thank you for your help
please find attached the annot file
I am using the 5.3 release
Angela
Would it be possible to send us your annoy file? Are you using
Hi Angela,
The issue has been fixed. It is because your annotation has 0's which is
corresponding to black color in the color table). I've made change in my
code so it doesn't display 0's. The fix will be in tomorrow's dev build.
If you are interested in trying it. You can download the dev
Would it be possible to send us an image file that you had problem with?
Best,
Ruopeng
On Feb 2, 2015, at 7:38 AM, Pernille Iversen pern...@drcmr.dk wrote:
Dear Freesurfer team,
We calculate our T1 images from quantitative sequences. I have tried to
process one of these images with the FS
Hi Xiuming,
I think the color scale always display the full scale which includes the
inverted part. I understand it is not ideal in this case. I will improve it.
Best,
Ruopeng
On Feb 6, 2015, at 8:26 PM, Xiuming Zhang (Ming) ericzhangxium...@gmail.com
wrote:
Hi Ruopeng,
Thanks a lot for
Hi Xiuming,
You can’t change color scale or change the background color from the
command-line. You can change the background color from the GUI: Edit -
Preferences. I will add these options in the command-line.
Best,
Ruopeng
On Feb 6, 2015, at 11:52 AM, Xiuming Zhang
I think you need to create 2 sets of way points as iso-lines. You can do
that from File - New Point Set and select 'way point'. Then you should
be able to use the line profile tool.
On 01/14/2015 04:55 PM, Albrecht, Daniel S. wrote:
Hello,
I'm having trouble using the line profile tool in
That option is only available in the development version of freeview.
You can try removing :annot_ouline=1 from the command-line and turn it
on manually from the GUI.
Best,
Ruopeng
On 01/15/2015 01:28 PM, Hirsch, Gabriella wrote:
Hello,
I have encountered a silly error message I'm hoping
I can confirm this bug on Mac (It does not happen on Linux). I'll look
into it.
Best,
Ruopeng
On 01/21/2015 03:11 PM, Mateus Aranha wrote:
Hi all,
I recently installed freesurfer on my mac, and I'm having a small
problem with freeview. If I load a segmentation file, and then try to
Hi Ronald,
No the issue is still there. I will let you as soon as it is fixed. The
default LUT is FreeSurferColorLUT.txt. But it is hard-coded into the binary.
Best,
Ruopeng
On 02/10/2015 12:03 PM, Ronald Pierson wrote:
When loading a lookup table in freeview on the Mac with version 5.3 the
What if you just load one surface:
freeview -f good_output/surf/lh.pial
Does it load?
Best,
Ruopeng
On 01/06/2015 03:23 PM, Hirsch, Gabriella wrote:
Hi,
I am trying to view surfaces in 3D using Freeview on my own subject
data via this command (replacing the subject name);
freeview -f
Hi Ronald,
This issue has been fixed. If you want to download the latest Freeview
build, please follow the instructions on the following page:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
Best,
Ruopeng
On 02/10/2015 12:03 PM, Ronald Pierson wrote:
When loading a lookup table in freeview
Can you try just loading one surface? Such as:
freeview -f /media/seagate_external/subject/surf/lh.inflated
Does it load? What if:
mris_info /media/seagate_external/subject/surf/lh.inflated
or even just:
ls -l /media/seagate_external/subject/surf/lh.inflated
Does it show any error?
On
Hi,
You can run the following command in a console to reset freeview settings:
rm ~/.config/Massachusetts\ General\ Hospital/freeview.conf
Then run freeview again.
Best
Ruopeng
On Mar 22, 2015, at 12:12 AM, zhaoshanshan shanshanzhao...@gmail.com wrote:
dear,
I have some problems
Yes, I think I fixed it.
On Mar 2, 2015, at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
I know that Ruopeng was fixing it a few months ago. Ruopeng, did you finish
that fix?
doug
On 03/02/2015 10:28 AM, Xiaomin Yue wrote:
Hi Doug,
thanks for your response. You are
Hi Xixi,
Do you want to create a customized annotation file to load on a surface?
or do you want to load multiple labels with different colors?
Best,
Ruopeng
On 06/16/2015 03:33 PM, Xixi Wang wrote:
Hi FreeSurfer users,
I’m trying to label different ROIs with corresponding decoding
Hi Joseph,
In freeview you can use Tools-Transform Volume to reorient volumes.
Best,
Ruopeng
On 08/11/2015 02:59 PM, Bruce Fischl wrote:
Ruopeng should be able to help you out
cheers
Bruce
On Tue, 11 Aug 2015, fmri wrote:
Is there a wiki instruction block on how to reorient all volumes?
Would it be possible to send me the surface and the volume that do not
align in freeview?
Thanks,
Ruopeng
On 08/13/2015 11:46 AM, Roan LaPlante wrote:
Hello,
I am trying to use mris_compute_lgi to create the smoothed pial
surface with no gyri, and then use this surface for a different
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