Hello. Freesurfer experts:
After autorecon3, Freesurfer generates the thickness measure of pre-defined
ROIs from Desikan’s parcellation. Now I want to make a picture illustration of
thickness but only with rostral middle frontal ROI. My questions are:
1 which surface would be fit for the
Hello, Freesurfer experts:
We are extracting the average cortical thickness of each hemisphere for every
subject using mris_anatomical_stats. We found that for one subject (attached
below), the thickness measures are quite similar but the “intrinsic curvature
index” differs drastically
Hello, Freesurfer experts:
I am using the mris_anatomical_stats to extract the average cortical thickness:
mris_anatomical_stats -l lh.cortex.label -f subject1.txt subject1 lh
the output is
number of vertices = 127190
total surface area = 84246 mm^2
] installation problem
the SetupFreeSurferEnv.csh file needs to be run. see installation
instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
n.
On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote:
Hello, Nick
I tried mri_convert work, glxgears,tksurfer, qdec
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] installation problem
does mri_convert work?
glxgears?
tksurfer?
qdec?
freeview?
your installation should work on ubuntu, as it has for other people, so
i'm a bit at a loss.
n.
On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote
Hello, Freesurfer experts:
I am new to freesurfer and try to
install the newest version of freesurfer in Ubuntu system. I closely
followed the instructions, and the only difference is that I
installed it in my Documents, instead of local folder.
Below
Hello, Freesurfer users:
I am new to Freesurfer. I have two questions when I tried to install the
Virtualtoolbox-Freesurfer into Window-XP system.
1) I downloaded the VirtualBox 4.0 for Windows hosts, but in the step of
“Adding the downloaded hard disk image”, there is no “Add” button
Hello, Freesurfer users:
I am new to Freesurfer. I have two questions when I tried to install the
Virtualtoolbox-Freesurfer into Window-XP system.
1) I downloaded the VirtualBox 4.0 for Windows hosts, but in the step of
“Adding the downloaded hard disk image”, there is no “Add” button
Hello, Freesurfer experts:
I found to report subcortical volumetric measure, ie, the volume of amygdale,
people tend to use icv as a control variable. Is there any corresponding
measure to correct the cortical thickness/area/volume results from autorecon3.
Because we have priori hypothesis
(if it isn't
already computed by recon-all in the most recent FS versions) or run the
command separately for the 'pial' and 'white' surfaces and then average
the resulting areas].
cheers,
-MH
On Fri, 2010-12-17 at 01:42 +0800, Liukarl wrote:
Hello, Freesurfer experts
Hello, Freesurfers
After autorecon3, there are cortical measures for the over 30 predefined
regions. And for each regions, there are area, volume, and thickness 3
different measures, which means there are approximately 200 measure for both
hemispheres.
As a preliminary analysis without
On Thu, 8 Apr 2010, Liukarl wrote:
Hello, Freesurfer experts:
I noticed for analyzing the results from autorecon2,
the intracranial volume are controlled as covariate in
some publications. Is there any corresponding
covariate for cortical results from autorecon3
Hello, Freesurfer experts:
I noticed for analyzing the results from autorecon2, the intracranial volume
are controlled as covariate in some publications. Is there any corresponding
covariate for cortical results from autorecon3, cortical thickness, surface,
and volume?
In my current
Hello,
I looked at the results from stage 3 and found out it has 1100 regions (we
might not use qdec since we have many other variables to control). But it is
beyond manageable levels. What we want might two things:
The first one might be a general measure of thickness (or volume) of
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