Hi,
I want to get a distance scale bar on tksurfer's window. I can get a very
dark bar on the black background, but I can't see any text around it. I
guess it is because the text is also black, which is buried under the black
background. Is there a way to change the text color?
Thanks,
Yang
I see. Thanks!
On Fri, Sep 16, 2011 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
I don't think there is text. The scale bar is 1cm long.
Yang Liu wrote:
Hi,
I want to get a distance scale bar on tksurfer's window. I can get a very
dark bar on the black background
is 128
On Fri, 16 Sep 2011, Douglas N Greve wrote:
I don't think there is text. The scale bar is 1cm long.
Yang Liu wrote:
Hi,
I want to get a distance scale bar on tksurfer's window. I can get a
very dark bar on the black background, but I can't see any text
around it. I guess
Hi Bruce,
'set scalebar_bright 240' works.
But when I type 'draw_scalebar',
it says 'invalid command name draw_scalebar.
Did I miss anything?
Yang
On Fri, Sep 16, 2011 at 11:57 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
at the tksurfer tcl prompt (%)
On Fri, 16 Sep 2011, Yang Liu
It worked. Thanks.
On Fri, Sep 16, 2011 at 12:06 PM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
hmmm, looks like it's not linked. Just try doing a redraw in the interface
and see what happens
On Fri, 16 Sep 2011, Yang Liu wrote:
Hi Bruce,
'set scalebar_bright 240' works.
But when I
Greve
gr...@nmr.mgh.harvard.eduwrote:
You're using a fairly old version of freesurfer. If you have to use this,
then use mkanalysis-sess (without the .new).
doug
Yang Liu wrote:
After I run recon-all -version, it shows: v 1.133.2.57 2009/08/06'.
Since we have a lot of scripts for the older
into a waveform. I'm not sure what you are
looking for if you want something that is equal to the number of time
points. What do you want to do with it?
doug
Yang Liu wrote:
Hi Doug,
As the freesurferwiki says, the h.nii contains the estimated hemodynamic
response at each voxel, along
Hi all,
I want to plot the hemodynamic response of a voxel after my analysis
finishes. I hope I can get the hemodynamic response of each voxel for each
session, so I can see the statistics by myself.
My analysis.cfg is below:
-gammafit 0 8
-gammaexp 0.3
-timewindow 40.
-prestim 0
-polyfit 2
to start the time window 4 sec before the stimulus onset and
stop it 20 sec after stimulus onset. Do not include -gammafit.
doug
Yang Liu wrote:
Hi all,
I want to plot the hemodynamic response of a voxel after my analysis
finishes. I hope I can get the hemodynamic response of each voxel for each
:
Yes, but don't use mkanalysis-sess.new. Are you not using version 5.X?
doug
Yang Liu wrote:
Hi Doug,
Thank you for prompt reply.
So I should remove '-gammafit', and add '-fir 4 24' is for
mkanalysis-sess.new?
Yang
On Tue, Aug 9, 2011 at 11:42 AM, Douglas N Greve
gr
Hi all,
I have a nifti file f.nii whose size is 80*80*60*266, (266 is the TRs).
Using mri_info f.nii, I can see that its orientation is is PIL. I want to
change it to RPI.
I do the following:
mri_conver --in_orientation PIL --out_orientation RPI -i f.nii -o
f.rpi.nii
It give me f.rpi.nii, which
Hi,
I was running selxavg-sess, and met this error:
$Id: fast_selxavg.m,v 1.40.2.2 2009/04/09 20:01:57 greve
Exp $
Parsing Arguments
RescaleTarget = 1000
UseMRIread = 1, ext = nii
Checking Parameters
??? Undefined function or variable xyzscale.
Error in == load_nifti_hdr at 138
with $env(VAR_NAME) I think
cheers
Bruce
On Tue, 26 Apr 2011, Yang Liu wrote:
Hi all,
I want to save the tiffs of different views automatically. I am trying to
use tcl script to do it.
My problem is that I need to pass the file's name that is being displayed
in
the tksurfer window
Hi all,
I want to save the tiffs of different views automatically. I am trying to
use tcl script to do it.
My problem is that I need to pass the file's name that is being displayed in
the tksurfer window to the tiff file that I want to save to.
For example,
I am running
tksurfer -f
Hi,
I am trying to paint the functional significance map onto the surface
generated from the antomical (monkey brain). What I am doing now is using
the following command:
tksurfer ${tmp_subj} ${hemi} ${cut_surface} -overlay
...@nmr.mgh.harvard.eduwrote:
Hi Yang, using mri_vol2surf is more accurate than tksurfer by itself. You
can also control the depth of projection with mri_vol2surf (eg, sample half
way between the white and pial surfaces).
doug
Yang Liu wrote:
Hi,
I am trying to paint the functional
Hi surfers,
I have two volumes, one is 96*96*50*272, and the other is 84*96*50*272. I
want to do motion correction between the two.
But I have to make their spatial size to be identical. Is there a command in
Freesurfer that can crop the size 96 to 84?
Thanks.
Yang
no longer
follow the boundary of the wm.mgz. If it did it would have a defect! You can
also look at the orig.nofix and/or the inflated.nofix to see where the
defect is in that region
cheers
Bruce
On Tue, 11 Jan 2011, Yang Liu wrote:
Hi Bruce,
I followed the tutorial at
http
macaque data, so I think there is no
aseg for that. I would love to be corrected on that point though.
Best
Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu liu.yan...@gmail.com wrote:
Hi Khoa,
Thanks for your reply.
I attached the snapshot of the same slice
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu liu.yan...@gmail.com wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz
is uchar. However, I found that the places surrounding the brain which have
0 grayscale values in the a.mgz
(for no scaling)
On Wed, 15 Dec 2010, Yang Liu wrote:
Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz
is uchar. However, I found that the places
Hi Doug,
The cerebellem and the pons are still in the filled.mgz. Are they supposed
to be completely gone in filled.mgz?
Thanks,
Yang
On Tue, Dec 7, 2010 at 10:48 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Did you look at the filled.mgz? Is it detached there?
doug
Yang Liu wrote
/Troubleshooting is a
little vague for me.
Are there further instructions (better with figure examples) available?
Thanks,
Yang Liu
PostDoc,
Wellesley College and HMS.
On Mon, Dec 6, 2010 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Have you looked at the filled.mgz volume
Hi,
I am processing the anatomical monkey brain now.
When recon-all runs, it stops at the step of mris_fix_topology
I inserted the last part of my recon-all.log below:
It stops at CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)
for more than 12 hours. Does this step take that long? Or
25 matches
Mail list logo
