See inline replies below. On 07/12/2011 02:10 PM, Colin Reveley wrote: > Hello - > > I'm having a segmentation difficulty. The aim is to register F99 > (macaque) against an individual. The individual was scanned ex-vivo, > so it's an MTR image rather than T1. So the contrast is kind of better > than T1 and that may, or may not cause issues with surefit. I've tried > segmentation many ways. > > the data is 0.25mm, so it is is downsampled to 0.5mm. there is a bias > field but I think it's corrected pretty well (using FAST, in FSL) and > the intensities are uniform. > > The MTR image has to be put into the correct orientation for caret, so > I register it to a deskulled F99. I've tried 6 parameter (I see no > need to scale it) and affine transforms. I transorm at 0.25mm (I > upsampled the deskulled F99), and then downsample for surefit. > > whatever I try, the result is the same as the figure attached, on the > right next to F99. > > I can tolerate most of the differences, but the issue at the rostral > end, where there is a fork in the frontal lobe towards the posterior > that is simply absent in F99, F6, wisconsin and all macaque > literature. It worries me a lot. It seems a lot of variation for macaque. I'm not certain which feature you mean, but I think it is the sulcus delineated by the aqua border, sandwiched between the more vertical lime-green and blue ones. Yes, it is more defined in your subject, but it strikes me as demanding more uniformity than is warranted, even for a macaque. > > In the left hemisphere, this problem is less pronounced, but I'd like > to use the right for obvious reasons. > > It seems like this is a difference in gross anatomy. So it's likely wrong. > > when looking at the surefit result, there is quite a bit of gray > matter that, it would seem, has no associated white matter, and hence > is rejected from the segmentation. > > I think it does have associated white matter (it must do), and the > problem is to do with the linear transforms and/or resampling. Or the > MTR, just maybe although I doubt it. > > In any case, I'd be grateful if you'd take a look. the region I'm > referring too should be clear from the figure. There's a missing > sulcus from my brain, Just looking at the surface on the left, it does indeed look like there is a tunnel under what is likely a fused sulcus in your segmentation. It might not be too hard to "un-fuse" the posterior branch of that sulcus with patching. Otherwise, your surface really looks pretty decent.
You can try peak tweaking (http://brainvis.wustl.edu/help/peak_tweaking/); however, I'd copy your anatomical to a different directory, because I'm not sure you're going to improve on this base segmentation. Doesn't hurt to try, though. > and one that shouldn't be there, in the frontal lobe above the > temporal tip. > > help appreciated. > > Colin, > > Sackler Centre > Sussex > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
