I would say delete that portion where the correspondence is shaky. If a portion of the sulcus is present in both and clearly in correspondence, leave that portion. Where in doubt, delete.
On 07/13/2011 09:57 AM, Colin Reveley wrote: > So, I have to retract this question; looking at a pial surface it > seems pretty clear that the image on the right is a sensible fiducial > surface for my data. That's just the anatomy. > > But the the question becomes: in landmark registration, where a > feature is missing in one surface and present in another, is it best > to draw a landmark where the sulcus *should* be on the surface where > it is absent (as in figure), or just remove that border from both > surfaces. > > I would have guessed the latter. I suppose one can try both. > > On 12 July 2011 20:31, <[email protected] > <mailto:[email protected]>> wrote: > > Send caret-users mailing list submissions to > [email protected] > <mailto:[email protected]> > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > <mailto:[email protected]> > > You can reach the person managing the list at > [email protected] > <mailto:[email protected]> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. segmentation for surf morphometry issue (Colin Reveley) > > > ---------- Forwarded message ---------- > From: Colin Reveley <[email protected] <mailto:[email protected]>> > To: <[email protected] > <mailto:[email protected]>> > Date: Tue, 12 Jul 2011 20:10:37 +0100 > Subject: [caret-users] segmentation for surf morphometry issue > 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. > > 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, 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
