No. At least for this particular subject, when I run recon-all it does not
create the noCCseg file. However, I have only been starting from autorecon2.
Does this make a difference? Also, I have just downloaded version 4.2...if I
run it using the new version will it create the files I need?
Hi,
In Qdec, what exactly does the area option measure? As I understand, qdec
does its calculations vertex by vertex, which makes sense in case of
cortical thickness. But if area refers to surface area how does that change
from vertex to vertex? Or is it calculating the area by ROI? Is my
under
Hello again,
My questions refer to the attached image.
The image is of the average subject I created from our subjects using the
"make_average_subject" command. As you can see, in an inflated view there
are many gyri and sulci looking structures that shouldn't be there. Clearly
something is not r
Oops, forgot the attachment.
On Tue, Feb 17, 2009 at 11:42 AM, Devdutta W wrote:
> Hello again,
> My questions refer to the attached image.
> The image is of the average subject I created from our subjects using the
> "make_average_subject" command. As you can see, in an inflated view there
> a
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As far as the first, This happens sometimes when you make your own average
subject. You just need to inflate it more. I will try to dig up an old
email I have on the commands.
As for the second, just click the redraW BUTTON
CARL SCHWARTZ
On 2/17/09 12:44 PM, "Devdutta W" wrote:
Oops, forg
below worked for us
carl schwartz
-- Forwarded message --
From: Bruce Fischl
Date: Fri, Sep 5, 2008 at 1:26 PM
Subject: Re: more inflation
To: Doug Greve
two things:
1. use -n , where the default is 10 (try 20)
2. -dist , where the default l is 0.1 (try something smaller, o
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of
the area of the triangles which touch that vertex .
The volume data associated with a vertex created for a subject is not
buggy in how it is calculated now. it is the area of the mid-point
between the white and pi
Is there now actually a "mid" surface available in between the white and
pial surfaces? (i.e., akin to Caret)? Or by "area of the mid-point" are
you just referring to the average at each vertex of the ?h.area and ?
h.area.pial "curv" files?
thanks,
-Mike H.
On Tue, 2009-02-17 at 13:17 -0500, Ni
It seems like the issue of whether or not to correct the volume when
mapping to fsaverage is akin to the choice of "modulated" vs. "non-
modulated" VBM, as it's called...
-MH
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
> Devdutta,
>
> The 'area' of a vertex on a surface in freesurf
I agree. The average looks fine, and the stuff at the bottom is because
we don't automatically redraw the graphics window. You need to click
redraw (or alt-r when the focus is in the graphics window) is you
obscure part of it.
cheers,
Bruce
On Tue, 17 Feb 2009 c...@nmr.mgh.harvard.edu wrote:
I think the area probably should be corrected to preserve the native area
of the subject, but as you say we haven't gotten to the correction yet.
On
Tue, 17 Feb 2009, Nick Schmansky wrote:
Devdutta,
The 'area' of a vertex on a surface in freesurfer is just the average of
the area of the trian
Hi Mike,
we don't generate the mid surface by default, but there is code around to
do so if you want to. You can use:
mris_expand -thickness lh.white 0.5 lh.midgray
to generate it I think.
cheers,
Bruce
On Tue, 17 Feb 2009,
Michael Harms wrote:
Is there now actually a "mid" surface ava
yes, it's the same, and modulated (or Jacobian corrected) is definitely
the right thing to do IMO
On Tue, 17 Feb 2009, Michael Harms wrote:
It seems like the issue of whether or not to correct the volume when
mapping to fsaverage is akin to the choice of "modulated" vs. "non-
modulated" VBM, a
Mike,
The 'area of the mid-point' calculation is made by averaging the ?h.area
and ?h.area_pial data files (the ?h.area file contains the area of the
white surface). This is done in recon-all using mris_calc, and
outputs ?h.area_mid.
Nick
On Tue, 2009-02-17 at 12:41 -0600, Michael Harms wrote:
I have epi data with a single slice at each time point and am trying to convert
it.
get MRIresample(): error inverting matrix; determinant is nan, matrix is: when
it tries
to resample the data. seems the single slice blows a fuse. i don't see a flag
to turn off
the resampling ? or other way ?
Dear all,
I installed freesurfer_Linux_centos4_x86_64-stable-pub-v4.2.0-full on
SuSE Enterprise (SLED 10.2), and ran recon-all. The process ran until
near the end, and then terminated with the following error:
*
.
Reporting on 49 segmentations
#
Thank you everyone for your answers. They have been very helpful.
Devdutta
On Tue, Feb 17, 2009 at 1:24 PM, Bruce Fischl wrote:
> I agree. The average looks fine, and the stuff at the bottom is because we
> don't automatically redraw the graphics window. You need to click redraw (or
> alt-r whe
hello there,
i have questions for Pedro Paulo de M. Oliveira regarding the upcoming
Brazilian FS course but cannot find his email address anywhere in the
archives or his announcement. also, do you know if there is another
upcoming course in the states, preferably on the west coast? thank
Hi,
What's the use of the % threshold (-p option) in mri_segment?
Thanks.
Bai
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Sam,
Pedro Paulo de M. Oliveira's email is:
ppj at netfilter.com.br
The original post is here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-
February/009688.html
with details here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule
A course is being off
I think it's not used any more
On Tue, 17 Feb 2009, Bai Xue wrote:
Hi,
What's the use of the % threshold (-p option) in mri_segment?
Thanks.
Bai
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We still have four places.
Sent from my Nokia phone
-Original Message-
From: Nick Schmansky
Sent: 17/02/2009 18:36:08
To: Sam Torrisi
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] brazil course
Sam,
Pedro Paulo de M. Oliveira's email is:
ppj at netfilter.com.br
The original
Devdutta, Nick, Bruce, Mike
I'm trying to understand these measures in terms of how they would map to
the brain physically.
Would it be correct that the size of the triangles touching a vertex would
be related to the amount curvature near a particular vertex and therefore
the amount of unfolding
Hi Darren
the curvature is related to the angles of the edges connected to each
vertex (also called the "angle deficit"). The surface area should just be
given by how much compression expansion the individual surface undergoes
when it aligns to a spot in the atlas. We'll compute it and correct
Here is a question related to this whole discussion (prompted by what
Darren wrote):
As a practical matter, have you found the localized (i.e., vertex-based)
measures of area and volume to be biologically useful and meaningful?
Have they been used in any published studies? (I don't recall seeing
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