Matt,
In v4.0, you can try the option -multistrip, which will attempt eight
different parameter settings running mri_watershed and will pick the best
one.
Nick
> Hello freesurfer gurus.
>
> Recently I was trying to do a fix on a brain that appeared to have a bad
> skull strip. The T1 was fine b
Xiangchuan Chen,
You might want to look at the slides downloadable from the top of this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
which contain pictures showing the meaning of 'curv' and 'sulc'.
Nick
> sulc = "average convexity" from our 1999 reconII paper. Essentially
> measu
Hi Chris,
I guess you might click on "Save Main Volume As...", and then "OK". In this
case, 257 COR- files would be created in the /mri folder. I happened to do it
once, and redid the whole edit work.
Xiangchuan
Start Of Original Message
Date: 2007-11-05Time: 10:0
sulc = "average convexity" from our 1999 reconII paper. Essentially
measures the depth/height of each point above the average surface.
curv = smoothed mean curvature.
jacobian_white = the jacobian of the spherical transform. Measures the
amount of distortion needed to warp a subject into regis
Hello freesurfer gurus.
Recently I was trying to do a fix on a brain that appeared to have a bad
skull strip. The T1 was fine but the brainmask volume came out almost
totally black, with the surfaces confined to some fuzziness in the corner
(appearing very strange in tkmedit). I attempted to fix
Hi all,
I am using Qdec to examine the anatomical differences between two groups of
subjects. The surface-based measures I can select are thickness, area,
area.pial, sulc, curv, and jacobian_white. Could anybody tell me what
anatomical features the later three (sulc, curv, and jacobian_white) a
yes, but I would copy the brainmask.mgz first to make sure you don't
regret writing over it.
On Mon, 5 Nov 2007, Chris Watson wrote:
So in place of I should place brainmask.mgz? I believe
that is the volume I saved over. It's unfortunate that I'll have to re-do the
edits to the T1.mgz volume
So in place of I should place brainmask.mgz? I
believe that is the volume I saved over. It's unfortunate that I'll have
to re-do the edits to the T1.mgz volume...
thanks,
Chris
Bruce Fischl wrote:
Hi Chris,
in the future you should just save over the .mgz files. So they were
saved directly
Hi Chris,
in the future you should just save over the .mgz files. So they were saved
directly in mri and not in a subdir? That means that there is only one
volume, not two (brainmask.mgz and T1.mgz), do you know which one it is? To
convert from cor to .mgz do:
mri_convert
cheers,
Bruce
Hello, this is my first time using Freesurfer.
I was making some edits to the brainmask.mgz and T1.mgz volumes, and
saved them and left Friday evening. I would like to continue making
edits today. How do I open these volumes so that they include the edits
I made? When I saved, 256 COR-files we
what kind of animation? You should be able to do this with a tcl script
in tksurfer, saving consecutive tiffs from slightly different viewpoints.
See the wiki page on the tksufer tcl commands.
cheers,
Bruce
On
Mon, 5 Nov 2007, Martin Kavec wrote:
Hi,
sorry to bring an off topic, but I coul
Hi,
sorry to bring an off topic, but I could not find a solution myself.
I was asked to prepare a short fly-by animation of a ?h.pial for a TV who
interviewed my boss last week. Would you have any recommendation on how to do
that? The ?h.pial is a mesh, which is ideal, because the surface of th
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