sure 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 anatomy:
tkmedit myla_anat orig.mgz -over
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 cechavarri...@gmail.comwrote:
I looked at the surface mask and it seems those 0-valued
!
Cesar
On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
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 subjects looks like
Greve
gr...@nmr.mgh.harvard.eduwrote:
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 the selxavg command below and
allow
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
On Thu, Dec 5, 2013 at 10:16 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
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:
Thanks for your help Doug
N Greve
gr...@nmr.mgh.harvard.eduwrote:
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 analysis to map out
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 compared against? I want to know to
make sense of the negative
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
...@nmr.mgh.harvard.edu 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 analysis for one of my subjects. I was
wondering
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,
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
, Cesar Echavarria wrote:
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
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
cechavarri...@gmail.comwrote:
I meant zoom in on the brain. I guess I'll take Doug's approach
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
Thanks,
Cesar Echavarria
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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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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
. 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 on x-axis, normalized
BOLD response on y-axis
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 attached image (time course on x-axis, normalized
BOLD response on y
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