Hi Ali,
On Jul 27, 2010, at 12:00 PM, Arslan, Ali wrote:
Hi,
I finished reconstructing a monkey's surface following the scripts on
the wiki. The output surfaces seems to be a bit distorted and rough
around the edges.
This reconstruction is done with a volume normalized by using ~400
white matter control points. The resolution of the scan is 1x1x1 mm.
Here are some pictures to look at:
http://www.flickr.com/photos/52445...@n05/sets/72157624471174691/
Are those real 1.0 mm isotropic volumes or 0.5 mm isotropic volumes
faked to appear 1.0 mm isotropic?
Interestingly, white matter and gray matter boundaries seem to be
intermingled for some reason. I was hoping control points would take
care of that problem but they didn't. This can be observed by the 2
vol_surf images in the set.
Can you post screen shots of the brain.final.mgz and brain.mgz?
The most obvious defects can be seen on the white matter. There are
small protrusions over the gyri, and the surfaces are generally very
rough, unlike a successful human reconstruction.
It pretty much looks like the segmentation in white and gray matter
failed badly for the final surface. Also notice how the initial segmentation
(wm.mgz) that produces the green line actually traces somewhere in between the
white and gray matter boundary? It pretty much looks like the normalization of
your images is not helpful for freesurfer. Alas, I have no real help to offer
right now (I am struggling with similar issues tight now). In case I find a
work around I might post a fresh set of processing scripts...
I was wondering if you have any ideas as to the source of the problem.
Skull stripping was done with FSL's bet, and it looks successful. Can
it be a problem with intensity normalization?
I agree, the normalization does not really work out. I have no solution
to offer right now. Well, except to have visually inspect the rawavg.mgz see
whether you think there is enough dynamic contrast inthere that you could trace
the white/gray matter boundary by hand. If yes, it should be possibly to
convince freesurfer to do it for you. If not then you will need new scans.
Best
Sebastian
Regards,
Ali Arslan
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