Hi,
Is there any way to run autorecon2-cp with an edited brain volume so that it
concurrently adjusts the pial surface. Everytime I try to run it, it seems to
erase my edits to the brain volume. Howeever, running autorecon2-wm or -pial,
uses the brain edits.
Some help on this would be much appre
Hi Alex,
I've looked into your problem and I do see what you mean. Here's a brief
run-down on the different flags.
-autorecon2-cp begins with -normalization2, using your control points.
Problem is it WILL write over the brain volume, creating a new one. It
then finishes the stream from her
If you don't have a surface, then don't run it with --surf. It's
important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
Dear Nick,
I recently installed the dev release from October 3rd, but tkregister2 still
does not work after autorecon1. (It will
How can I check the registration if I can't see the surface?
-Sasha
>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>>
If you don't have a surface, then don't run it with --surf. It's
important to have an accurate talairach.xfm.
doug
On Mon, 17 Oct 2005, Sasha Wolosin wrote:
> Dear
Good question! I am hoping to have an answer for you soon...
On Tue, 2005-10-18 at 12:11 -0400, Sasha Wolosin wrote:
> How can I check the registration if I can't see the surface?
> -Sasha
>
> >>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>>
>
> If you don't have a surface, then don't
Hit the "compare" button to flip back and forth between the talairach
brain and your subjects anatomical.
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
How can I check the registration if I can't see the surface?
-Sasha
Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>>
If you don't have
recon-all -cortparc -aparc2aseg ...
On Mon, 17 Oct 2005 [EMAIL PROTECTED] wrote:
Hi, I just updated the freesurfer. I have processed a large amount of
data using older recon-all. I just found that aparc.annot generated by
oldered and newer recon-all are different. I want to generate new
ap
My subject's anatomical scan seems to be relatively well aligned with
the fuzzy talairach brain, but the green 'orig' surface is completely
off. How is this possible? Why do we need the surface at all if it's
not used for alignment?
The tutorial advises using the 'final objective function
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
My subject's anatomical scan seems to be relatively well aligned with
the fuzzy talairach brain, but the green 'orig' surface is completely
off. How is this possible? Why do we need the surface a
Sasha,
We are updating our tutorial to make it clearer how and when to correct
a bad talairach alignment. The tutorial assumed that recon-all -
autorecon-all was run, which would have created surfaces (which might
not have been fully correct, but good enough to check talairach
alignment).
In you
yes, the surface does not align with the anatomical.
>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 2:20 PM >>>
So the surface does not align with the anatomical?
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
> My subject's anatomical scan seems to be relatively well aligned
with
> the fuzzy tal
OK. We've replicated this problem here. I'll work on it to find out
what's going on.
doug
On Tue, 18 Oct 2005, Sasha Wolosin wrote:
yes, the surface does not align with the anatomical.
Doug Greve <[EMAIL PROTECTED]> 10/18/2005 2:20 PM >>>
So the surface does not align with the anatomic
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