Hello,
I am trying to calculate the percent signal changes for my monkey data.
I did this by running the command selxavg3-sess and looking at the cespct
values (or equivalently by using h.nii divided by h-offset.nii).
I found in the mailing list that this value should be corrected by a scaling
f
perhaps an alternative is to use the surface area measure of an ROI,
namely the aparc regions, to conduct a group analysis, as the vertex
distribution problem is averaged-out over the region.
n.
On Wed, 2010-09-29 at 21:02 -0700, Don Hagler wrote:
> The area maps do contain the actual surface are
Jeff,
Posting this back to the list so that others can see your reply.
cheers,
-MH
Forwarded Message
From: Jeff Sadino
To: Michael Harms
Subject: Re: [Freesurfer] Surface Area and Cortical Volume
Date: Wed, 29 Sep 2010 17:29:45 -1000
Hi Michael,
After reading your answer, I
Hi Thomas, you may have found a bug in my scale factor calculation. Can
you compute the new scale factor as described below? BTW, these issues
are fixed in version 5.
cd bold/analysis
x = load('X');
tirf = x.flac0.ev(3).tirf;
Xirf = x.flac0.ev(3).Xirf;
scalefOld = sum(Xirf .* repmat(tirf,[1 size
Hi,experts,
I am trying to get the total surface area of pial surface using the following
command,but it seems the default surface for this command is white matter
surface, is there any parameters i could change to get the information from
pial surface ?
mris_anatomical_stats -l lh.cortex.la
usage: mris_anatomical_stats [options] []
So, just end your command with the word 'pial'.
cheers,
-MH
On Thu, 2010-09-30 at 17:09 +, Zhang, Yuning wrote:
> Hi,experts,
>
> I am trying to get the total surface area of pial surface using the
> following command,but it seems the default s
Does the surface area calculated here include the non-cortical area along the
medial wall ?
Thank you very much.
From: Michael Harms [mha...@conte.wustl.edu]
Sent: Thursday, September 30, 2010 5:24 PM
To: Zhang, Yuning
Cc: freesurfer@nmr.mgh.harvard.edu
S
you need to use the ?h.cortex.label with -l to exclude those areas.
On Thu,
30 Sep 2010, Zhang, Yuning wrote:
> Does the surface area calculated here include the non-cortical area along the
> medial wall ?
>
> Thank you very much.
>
>
> From: Michael Harm
It'll be the surface area of whatever you specified by the -l flag -- in
your case everything that is part of lh.cortex.label. You can view
exactly what that includes on tksurfer. Doing so, you'll see that the
non-cortical area along the medial wall is excluded.
cheers,
-MH
On Thu, 2010-09-30
Thanks, it is really helpful !!
best
yuning
From: Zhang, Yuning
Sent: Thursday, September 30, 2010 6:23 PM
To: Michael Harms
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] calculate the surface area of pial surface using
mris_anatomi
Dear Freesurfer experts
I am new Freesurfer user, I used the command:
tksurfer fsaverage lh inflated -annot aparc.annot
In the graph showed in the window are only the vertices, not surface, see
the figure in the attachment.
how to displace the surface in the window, which operation do I need ?
Hi,
I was wondering if it were possible/advisable to use data processed and
cached using earlier versions of FreeSurfe with the new 5.0 QDEC, since it has
enhanced capabilities.
Sincerely,
Mira
Mira Michelle Raman
Scientific Programmer
Center for Interdisciplinary Brain Sciences Research
Stan
Dear Mira,
I posted a similar question some days ago. It seems to be possible to
use the new qdec version for the group analysis for data that has been
processed and cached with version 4.x (at least 4.05 and newer).
Check this posting in the mailing archive:
http://www.mail-archive.com/frees
yes, you may use v5 qdec with prior processed data.
n.
On Thu, 2010-09-30 at 21:04 +0200, Christian Scheel wrote:
> Dear Mira,
>
> I posted a similar question some days ago. It seems to be possible to
> use the new qdec version for the group analysis for data that has been
> processed and ca
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