Hi Donna, Thanks again for the suggestions. I decide to chagne to PALS_B12. Is there an PALS_B12 dataset that are in native space (structural volume scans)?
I wanna use Freesurfer to generate the surface version of PALS_B12, and then cut & flatten the patches, and then use CARET to do the landmark-based warping. (I would like to select some landmarks on the individual patch & on the PALS_B12 patch) Cheers, jackie Am 29.08.2007 15:12 Uhr schrieb "Donna Dierker" unter <[EMAIL PROTECTED]>: > Hi Jackie, > > See inline replies below. > > Donna > > On 08/29/2007 07:16 AM, Chuan-Chih Yang wrote: >> Dear list, >> >> I got a question about the selection of target space (mapping volumes onto >> surface). My attemp is to map the functional zstat.nii of FSL onto N27 >> template by using caret. I found different target spaces that I can choose >> from in the 'atlas surface selection' window, >> > I hope you have a good reason for selecting Colin as the target surface, > rather than PALS_B12. >> in my case--- the zstat of individual in not yet normalized to any space, >> but the group zstat is already normalized to MNI 305,by FLIRT. I am >> wondering which target space and altas shall I choose, if I wanna normalze >> the zstat from FSL onto N27? >> > We don't have a version of Colin that was normalized using FLIRT (linear > affine), but we do have versions of colin in SPM99 and SPM2 space. (See > http://brainvis.wustl.edu/help/pals_volume_normalization for an > explanation of how methods and spaces relate in our terminology.) You > could use one of these for your group results, but I'd really recommend > using the PALS_B12 FLIRT surface as your mapping target for those group > results. > > For your non-normalized individual results, you really can't use any of > our atlas targets -- colin or PALS_B12. If you want to map the native > individual results, you'll need to segment his/her structural volume and > map to the individual's surface. >> Is there any difference between mapping the individual zstat and the group >> zstat from FSL onto N27? > Absolutely: Mapping individual results to colin -- even normalized > results -- is a bad idea. Even mapping normalized individual results to > PALS_B12 surface isn't a great idea. Mapping individual results to its > own surface reconstruction is a good idea. > > Mapping group results to colin is no longer recommended, because of the > limitations inherent in a single subject target. Colin has strange > anatomy in some places that cause undesirable mapping results in some > areas (e.g., left posterior STS and IPL). > > Mapping group results to PALS_B12 is the recommended option. > > If you're interested in seeing how the individual's results differ from > the group's, then I can think of two ways to accomplish this, but please > be advised that I'm not experienced in these kind of analyses, so I > don't know if a reviewer would be happy with them: > > * Normalize your individual to the same target used for your group > results. Compute the difference in volume-land. Map the difference > volume to the PALS_B12 FLIRT surface. Consider using the MCW BrainFish > algorithm. > > * Normalize your individual to the same target used for your group > results; reconstruct your individual's surface; map the individual zstat > to the individual's surface; and register it to PALS_B12. Map the group > zstat to the PALS_B12 FLIRT surface. Use Attributes: Metric: > Mathematical Operations to subtract one from the other (or > caret_command's new metric math, if you have the latest and greatest > command line utility). > > Either way, you're guaranteed to get lots of clusters of differences; > however, I'm not sure how you'd establish significance criteria. Any of > the 12 Buckner subjects that contributed to PALS_B12 will have such > clusters where its individual surface differs from the PALS_B12 group > target (i.e., normal anatomical variability is pretty high in humans). >> (is there a availble N27 altas that is FLIRTed into >> MNI305 ? ) >> > No. You may have a good reason for using Colin, but I'd like to know > what it is. >> Thanks much for the help! >> >> Cheers, >> jackie >> >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users >> >> > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
