Sorry that I keep on asking questions but I want to know if using a model
can significantly increase the chance of getting a significant response.
As far as I see for the positive peak, when I use a model (e.g. gamma
model or spmhrf), I see a more significant response compared to when I use
t
Hi Jon, I don't know how to make this work, but I'm sure that those
commands will not do it. Sorry:(
doug
On 4/10/13 1:13 PM, Jon Wieser wrote:
> we captured some dti data. there were 2 runs. we acquired in the axial plane,
> 2mm slice thickness the first run captured the lower half of the b
Hi Chris
the easiest way would be to load the surfaces and parcellation in in matlab
and look for adjacency that way
Bruce
On Wed, 10 Apr 2013, Chris McNorgan wrote:
> Hello Freesurfers,
>
> I was wondering if there is information embedded in the annotation/label
> files that could be used to d
yes, that is what you want. The only other way that comes to mind is to
model each event type as two event types one delayed relative to the
other. Then model the responseto each as a gamma. If the delay is right,
then the first gamma should model the main positive response and the
second gamm
If you run tkmedit-sess, then open the overlay configuration window,
then advance the time point to the delay you want. Otherwise, you can
create a contrast where you just look at the delay you want. To do this,
run mkcontrast-sess with -setwdelays and specify 0 for all delays and 1
for the de
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I think I figured it out but I want to double check. I am generating
group-average map for my subjects using isxconcat-sess command which
generates ces maps for each time frame. I think these maps are what I
wanted. Right?
If you still have other solutions that you think may generate more
reliab
That's the problem Doug. I have already generated the FIR model but how can
I show the sig MAP for one "particulat time point". What are the other
ways?
On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
wrote:
> Hi Shahin, there are several ways that you could do it. The one that
> immediately c
Hi Shahin, there are several ways that you could do it. The one that
immediately comes to mind is to use an FIR and then test for a
difference at a particular post stimulus time point.
doug
On 04/10/2013 03:54 PM, SHAHIN NASR wrote:
> Hi,
> I want to generate a map to show the significant
Hi,
I want to generate a map to show the significant difference between
HRF undershoot (negative peak of activity) between two conditions
independent from the positive peak. Is there anyway, to generate this map?
P.S.: Please note that I need a map and not a time course graph.
--
Shahin N
You can do that, but you'll need to change the paradigm file to reflect
the new timing.
doug
On 04/10/2013 01:57 PM, preci...@nmr.mgh.harvard.edu wrote:
> If anything I was thinking of removing the first two time points, as those
> are going to get nixed anyway. I was hoping it wouldn't come to th
If anything I was thinking of removing the first two time points, as those
are going to get nixed anyway. I was hoping it wouldn't come to that but i
f that's the only way...
-Ronny
> Hi Ronny, the time point used to as the template is hard-coded to be the
> middle time point. If this is just the
Hi Ronny, the time point used to as the template is hard-coded to be the
middle time point. If this is just the case for one subject, a silly but
simple solution is to remove the last two time points from the time
series. This will cause the "middle" time point to shift to an earlier
time point
One of my subjects exhibited motion during the middle time point of one
the functional scans. FS-FAST then reads all other time points as having a
significant amount of motion because the subject was out of place during
the point that is marked as the origin. Is there some way that I can set a
diff
Daniel,
We're repeating our paired-analysis of thickness measures between 5.1
and 5.2. In the meantime, to check for correctness, open the
brain.finalsurfs.mgz file with the surfaces overlayed, and check the
intensity value of the voxels which appear to be non-cortical 'black
spaces', relative to
we captured some dti data. there were 2 runs. we acquired in the axial plane,
2mm slice thickness the first run captured the lower half of the brain, slice
locations: I56-S20, and the second run captured the upper half of the brain
S16-S92. i have made briks from each of these runs.
I can conver
Hello Freesurfers,
I was wondering if there is information embedded in the annotation/label
files that could be used to determine whether two labels represent
anatomically adjacent regions? For example, I have parcellated a bunch
of participants using connectomemapper into 1000 ROIs. I was just
Hi Gonzalo,
You can untar the 5.2 files in a separate directory, and then just source
the SetUpFreeSurfer.csh from the directory of the version of FreeSurfer
you want to use. You can run 'which recon-all' to check which version you
have sourced.
-Louis
On Wed, 10 Apr 2013, Gonzalo Rojas Cost
Hi:
How can install version 5.2 in a computer without uninstalling
version 5.1 ?...
Sincerely,
--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771
Ok, I'll try to put together a stat from aparc too.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
On Wed,
Hi PPJ,
Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any
chance you could also provide the cortical thickness of the 2009 atlas (e.g.,
rh)?
I will take a look into the aseg.volume in my data too.
Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yal
Hi Daria - How much memory does your system have? Were you ever able to
run trac-all from the 5.1 version on the same system?
a.y
On Wed, 10 Apr 2013, Antonenko, Daria wrote:
> Hi FS experts,
> I tried to run Tracula with the new FS 5.2 release and came across memory
> allocation problems in
Hi PPJ
That's exactly what we are doing. Good to hear its stable for you
Bruce
On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira
Junior wrote:
> I have processed more that 600 brains with both versions in the last weeks
> and the only difference I'm seeing between version 5.2.0 a
I have processed more that 600 brains with both versions in the last weeks
and the only difference I'm seeing between version 5.2.0 and 5.1, besides
the obvious new features, is processing time.
Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.
Besides that there's no visible differen
We are investigating it. I did fix one thing that you can try if you want -
give us your hardware/software info and we will send you a new version of
mris_make_surfaces
Bruce
P.s. you can also upload and we will take a look
On Apr 10, 2013, at 6:11 AM, "Yang, Daniel" wrote:
> Dear FreeSurfe
Dear FreeSurfer Experts and Users,
Did anyone find similar things using FS 5.2 (please see my previous post
below)? That is, FS 5.2 is including more non-cortical "black spaces"
within pial surfaces, compared to FS 5.1?
I'm not interested in nitpicking but I feel this is a rather serious
issue, s
Hi list,
I'm performing cortical thickness among 3 groups by using GLM.
I created a group descriptor file with 3 groups and 2 covariates (age and mean
thickness).
I performed 3 comparisons A-B, A-C, B-C.
Now, for one of 3 groups (group C) I have:
groups C=30 subjects; I'd like to divide it in some
No I did not try it. Now I'm trying to perform it.
Thanks,
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 9-apr-2013 17.50
A:
Cc:
Ogg: Re: [Freesurfer] R: Re: incomplete tracts
Hi Stefano - Did you try CVS for the inter-subject registration? It
doesn't look
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