Hi freesurfers,
Anyone know what the scale bar in TkSurfer represents? From past threads I
gathered that it represent 1 cm on the human brain. However, the size of
the bar displayed gets smaller as I scale the brain up which does not make
sense if the bar is supposed to represent a constant length
I meant zoom in on the brain. I guess I'll take Doug's approach and
estimate the scale of the bar with the xyz coordinates.
Cesar
On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl
wrote:
> Hi Cesar
>
> what do you mean by "scale the brain up"?
>
> Bruce
>
&
Actually, Doug can you tell me how to get the xyz coordinates on Tksurfer
so I can figure out the length of the bar as you did?
Thanks
Cesar
On Fri, Nov 22, 2013 at 12:19 PM, Cesar Echavarria
wrote:
> I meant zoom in on the brain. I guess I'll take Doug's approach and
> estim
Hi all,
I'm running a retinotopy analysis. I was wondering if there was a way for
me to ignore the last x seconds/TRs of a given run. I want to ignore this
bit of time because each run started and ended with a 'blank screen'
period.
I appreciate any tips you guys might give me.
Cesar
Hi all,
I'm running a retinotopy analysis and I was wondering if there was a way
for me to ignore the last x seconds/TRs of a given run. I want to ignore
this bit of time because each run started and ended with a 'blank screen'
period.
I appreciate any tips you guys might give me.
Cesar
_
Hi freesurfers,
I conducted a retinotopic analysis for one of my subjects. I was wondering
if any of you knew what is represented by the values in the sig.nii file
under the 'polar' directory that the process puts out.
I appreciate your help!
Cesar
___
Greve" wrote:
> It is the -log10(pvalue) where pvalue is the p-value from the F-test
> of the real and imaginary components
> doug
>
>
>
>
>
> On 12/03/2013 05:41 PM, Cesar Echavarria wrote:
> > Hi freesurfers,
> >
> > I conducted a retinotopic
t;
>
>
> On 12/03/2013 06:21 PM, Cesar Echavarria wrote:
>
>>
>> So I want to figure out which voxels were modulated significantly by the
>> orientation of our stimuli. Is this the right file to look at? If so what
>> are the real and imaginary components comp
N Greve
wrote:
>
> sorry, there should be an fsig.nii.gz which is the F test of the real and
> imaginary. That sounds like what you are asking for
>
>
> On 12/04/2013 12:19 PM, Cesar Echavarria wrote:
>
>> To clarify, I am piggy-backing on the retinotopic analysi
Thu, Dec 5, 2013 at 10:16 PM, Douglas Greve wrote:
>
> To get the F test, you will need to put the runs from both sessions in the
> same bold folder (and make sure to use -per-run registration)
> doug
>
>
>
>
>
> On 12/5/13 4:42 PM, Cesar Echavarria wrote:
>
Hi freesurfers,
I have run 2 separate blocked fMRI experiments ,each on a different pool of
subjects, with couple of conditions identical in both experiments. I would
like to pool the data for the conditions in common across these 2
experiments/group of subjects. I was wondering if anyone had any
hanks!
Cesar
On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl wrote:
> Hi Cesar
>
> what command lines did you run to register and sample?
>
> Bruce
>
> On Mon, 5 May 2014, Cesar Echavarria wrote:
>
> Hello freesurfer experts,
>> The functional overlay for one of our sub
las N Greve
wrote:
> It could be that the brain mask is too aggressive. Try looking at
> Subjects/myla/bold/RRR/masks/brain.nii.gz
>
> doug
>
>
>
> On 05/05/2014 03:17 PM, Cesar Echavarria wrote:
>
>> Hi Bruce,
>>
>> After unpacking the data, I simply run t
e that the activation
> is exactly 0? Also, look at cortex.label to check whether somehow those
> vertices were not labeled.
>
>
> On 05/05/2014 04:08 PM, Cesar Echavarria wrote:
>
>> I used the command below to check the brain mask relative to the
>> subject's
holes" on the surface mask. Is there anything we can try with the
bbregister command to prevent it from getting stuck in local minima or the
like?
Thanks
Cesar
On Tue, May 6, 2014 at 4:44 PM, Cesar Echavarria wrote:
> I looked at the surface mask and it seems those 0-valued vertices are
h other. I plan to
then make a label file in which these vertices are listed.
Please let me know if you have any insight into how this might be done.
Thanks,
Cesar Echavarria
___
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Hello,
Anyone know of a fast way to get the talairach coordinates of a vertex
index in fsaverage. A function or script is best since I want to do this
for a large number of vertices.
Thank you for any help you guys can provide.
Cesar
___
Freesurfer mail
lpful
Thanks,
Cesar Echavarria
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe t
Hi Freesurfers,
I want to look at activity in my subjects' retina for one of my
experiments. I did volume-based analysis in freesurfer version 5.3 but I
noticed that activity outside of the brain has been masked. Is there an
option somewhere along the processing pipeline to prevent masking of
acti
You have to model the return to baseline even if you
> are not interested init. Try that and get back to me if it does not work.
> doug
>
>
> On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
>
>> Hi Doug,
>>
>> As you can see from the attached image (time course
> would be --fir 4 22. You have to model the return to baseline even if you
> are not interested init. Try that and get back to me if it does not work.
> doug
>
>
> On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
>
>> Hi Doug,
>>
>> As you can see from the at
Hi freesurfers,
I have an event-related design experiment which outputs a file with a line
corresponding to every TR.
i.e. for TR = 1 the first 3 columns of the file look like:
0 0 1
1 0 1
2 0 1
3 0 1
4 0 1
5 1 1
6 1 1
7 1 1
8 1 1
9 1 1
Assuming I have 5 seconds of fixation followed by second
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