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/52445793@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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