Hi Tom,
What kind of scans are you working with? How were
they collected? Have you averaged more than one
acquisition?
Jenni
autorecon2 ran all the way through. I first noticed a problem because
the wm.mgz file is only a narrow band of voxels and its distorted. The
brain.mgz file is missing some areas of white matter. aseg.auto.mgz is
missing a hemisphere, and aseg.mgz is very similar in shape to wm.mgz, which is
an irregularly shaped blob that occupies about 1/4 of the coronal section, and
is roughly centered in the image.
I am fairly certain that the
failure occured in the step generating aseg.auto.mgz or one of the steps just
prior, because nu_noneck.mgz looks good.
I created brainmask.mgz and
brainmask.auto.mgz using manual thresholding and they are exactly to my
specifications. Strangely, the output file brain.mgz still has
problems. It looks exactly as it did before manual thresholding.
on
a previous post to the list, it was suggested that default thresholding took
over because brainmask.mgz and brainmask.auto.mgz do not match. I assure
you that they do match. I cop[ied the mask that I manually created so that
both files match exactly.
-tom
On 4/13/06, Jenni Pacheco
<jpacheco@nmr.mgh.harvard.edu>
wrote:
Hi
Tom,
We're going to need a little more info. Did autorecon2
finish? Did it
fail part way through? When you say
everything has problems, what kind of
problems?
go here to see the
types of information we need in order to best help you:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
thanks,
--
Jenni
Pacheco, M.A.
Massachusetts General Hospital
Athinoula A. Martinos
Center for Biomedical Imaging
Bldg. 149, 13th Street, CNY
2301
Charlestown, MA 02129
jpacheco@nmr.mgh.harvard.edu
On
Thu, 13 Apr 2006, Tom Bayer wrote:
> I'm having problems with the
output of recon-all -autorecon2. proceeding
> down the
recon-all dev table, I checked the outputs of each step.
> everything
looks good until aseg.auto.mgz everything after has
problems.
> What kind of manual intervention do I need to do for this?
>
> -Tom
>