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
24" 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
>&
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
las N Greve
wrote:
> 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 ha
aveform. 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
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 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
>> dar
bar_bright 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
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
wrote:
> at the tksurfer tcl prompt (%)
>
> On Fri
It worked. Thanks.
On Fri, Sep 16, 2011 at 12:06 PM, Bruce Fischl
wrote:
> 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_bri
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? O
/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
wrote:
> Have you looked at the filled.mgz volume to make sure that cerebel
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
wrote:
> Did you look at the filled.mgz? Is it detached there?
>
> doug
>
> Yang Liu wrot
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
>
> 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 conform
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,
gt;
> This pretty much looks like 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 wrote:
> >
> >
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl
wrote:
> Then I must be a topologica defect
>
>
>
> On Jan 10, 2011, at 10:37 PM, Yang Liu wrote:
>
> Hi Sebastian,
>
> Yes. It is Macaque. There is no aseg.
>
> Yang
&g
the boundary is well defined in the slices.
Yang
On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl
wrote:
> Not without scrolling through the wm volume. You will need to edit it. Have
> you done the troubleshooting tutorial?
>
>
>
> On Jan 10, 2011, at 10:48 PM, Yang Liu wrote:
>
ion to correct a defect the orig (green) surface can 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
>>
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
__
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
/space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/si
:
> 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
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 $surface_fi
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 th
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
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, wh
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