Hi Danny, See inline replies below.
Donna > Hi Donna, > > thanks for getting back to me quickly :) > > I forgot to mention. I created the surface from a T1 image of a preterm > baby > brain. I managed to segment the white matter via utilizing Freesurfer to > get > the bias-corrected T1 normalization image and Brainvisa's anatomic > pipeline > to acquire wm/gm masks. Then I used SPM to extract the WM mask from the > gm/wm mask. When the mask came out it resembled a paintball blast mark and > had the ventricles and the thalami/basal ganglia structures not > highlighted > so I did some very quick manual correction. > > and thus the freakish surface was born :) Okay. Someday Freesurfer may segment baby brains, but currently the contrasts properties of the baby brain make this a suboptimal solution. > > THANKS for letting me know about the surface being registered to the > 711-2B > space and about the ROI volumes. Even we haven't tried auto-landmarks on baby brains, and we have no immediate plans to do so. Nor do we register baby brains to 711-2B. We do have some baby atlases we use. > > I'll see if I can register the images to 711-2B space to see if there is a > difference. Also I'll try to spend more time in manually filling in the > ventricle and correcting the segmentation. This segmentation seems beyond manual patching to me. > > btw, I saw from the Caret's wiki page that the lab is collaborating with > Terrie Inder's group in studying Human cortical development. > How did you acquire that developing cortical surface image on the wiki > page > (see attached), b/c that looks really good. Jason Hill (MSTP student who has completed PhD work and is now in clinical rotations) and Andy Knutsen (preparing to defend his thesis) developed an algorithm called LIGASE to segment the baby brains. They still needed some manual patching, but the quality was pretty good, if not excellent. I'm pretty sure they used the T2, rather than the T1. We are in the process of addressing reviewer comments on a paper describing these methods and the term control atlas Jason produced. We hope to have a citation for you soon. Maybe David will post his SfN poster on our ftp site. It covers this work. If you are serious about generating surfaces of baby brains, getting LIGASE might be worth your while. It runs on matlab. I think there may be some documentation. Jason is super busy and not as available as he might wish to answer user questions, but I can promise the resulting segmentations and surfaces are nearly as pretty as the city where you live. > > > > Cheers, > > > Danny Kim > Brainmapping > Dept. of Neurology > BC Children's Hospital > Vancouver, BC > > > On Thu, Oct 29, 2009 at 1:45 PM, Donna Dierker > <[email protected]>wrote: > >> On 10/29/2009 02:39 PM, Danny Kim wrote: >> > Hi fellow caret users, >> > >> > This is my first time posting a question to the mailing list. Forgive >> > me if I leave out anything important or formality. I'll try to include >> > everything I know. >> > >> > so I've been trying to landmark and paint the sulci of this brain (see >> > attached photos of Lateral and Medial view of resulted fiducial and >> > inflated surfaces). >> Well, it's almost Halloween, so I guess scary images are seasonally >> appropriate. But I must say, that is a pretty hideous fiducial surface >> you have there -- lots of appendages and handle-like spindles. Did you >> tessellate something like a FSL fast segmentation? >> > >> > I keep getting paint Sul.CeS not found and the automatic landmark >> > labeling does not go to finish in surefit segmentation. >> I just got that error today myself. In my case, it was because I was >> running auto-landmarks and feeding it a bad Depth column-name/number. >> But you might also see that error if your spec file has more than one >> anatomical volume in it. It just always seems to be that error whenever >> auto-landmarks fails. >> >> In your case, I can't be sure what caused it to fail. It could be that >> your surface isn't in 711-2B stereotaxic space. Eventually, we'd like >> to add handling to make the process of getting surfaces into 711-2B more >> seemless. But we're not there yet. >> >> But really you're going to have to improve the quality of the >> segmentation that generated this surface before registeration makes >> sense. >> > >> > How does the automatic paint generation of the core6 landmark, and >> > other sulci labels actually work? By my understanding, Caret, once it >> > finds the sylvian fissure correctly, should be able to locate the >> > central sulcus shouldn't it? and after that it should find all the >> > other sulci paints by using the B12 atlas. >> This isn't really documented/published anywhere, as far as I know. I'll >> give you my oversimplified take on it: The surface must be in 711-2B, >> so that the probabilistic volumes in your >> $CARET_HOME/data_files/sulcal_identification directory align properly >> with it. Several ROI volumes (e.g., CeS, HF, SF) are mapped to the >> surface, thereby forming surface ROIs, which are intersected with >> thresholded Depth metrics to pinpoint the location of key anatomical >> structures. Borders are drawn and trimmed to our Core 6 landmark >> specifications. >> > thank you all for any suggestion/input/critique! >> > >> > >> > Cheers, >> > >> > Danny Kim >> > Brainmapping >> > Dept. of Neurology >> > BC Children's Hospital >> > Vancouver, BC >> > >> > >> > ------------------------------------------------------------------------ >> > >> > >> > ------------------------------------------------------------------------ >> > >> > >> > ------------------------------------------------------------------------ >> > >> > >> > ------------------------------------------------------------------------ >> > >> > >> > ------------------------------------------------------------------------ >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > 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 >> > _______________________________________________ > 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
