On 10/14/2010 03:29 PM, Bruno L. Giordano wrote: > Hi Donna, > >>> 1. create a target surface from the SPM-normalized T1s of each of the >>> participants: this is not a very nice representation, but it shows >>> very clear landmarks (with the possible exception of the ventral >>> medial wall); >> So far, so good. What software will you use to generate the surfaces? > > My description was incomplete: I meant average the > participant-specific SPM-normalized T1s to create a group-average T1. > Then create a target surface by segmenting this group T1 with Caret. > This surface will obviously look bad. However, it still has each of > the default landmarks very clear. This target surface will be improved > at point 3. Segmenting group averaged MRI is usually a bad idea. >>> 2. project the surfaces of the participants (derived from >>> SPM-normalized T1s) onto this target surface; >> This isn't really clear. As best I can discern, you mean register your >> subjects to the PALS-B12 target atlas, at which time your various coord >> files, including fiducial/midthickness coord files, will get resampled >> onto the PALS-B12 73730 standard mesh. > See above. >>> 3. create a new improved target surface by averaging those coming out >>> from 2. (eventually include the additional temporal landmarks at this >>> point and not at 1.). >> Why? What is your motivation for creating a customized target, instead >> of using PALS-B12? What is different about your subjects? > > My thought is that by using a target surface that actually comes out > from my subjects the quality of the functional-to-surface mapping will > be improved, especially if I do the points 4-6. below: > >>> 4. project the surfaces of the participants used at 2. on the new >>> target; >>> 5. average surfaces coming out at 4; >>> 6. project my functionals (group results) onto the average surface >>> from 5. No, I am not convinced you will significantly improve your outcome this way.
If I understand you correctly -- and I'm not sure I do -- you still plan to segment your individuals and register their surfaces to some target. The question is what the target should be. I remain unconvinced that there is benefit to be gained by generating this customized target. I don't think tightened correspondence across nodes will offset the loss of benefit of using the PALS-B12 target (e.g., availability of several published parcellation schemes, borders, fMRI results from published studies, left-right correspondence). Now if you were not segmenting/registering your subjects, but rather just mapping their group results on some average fiducial surface, then I do acknowledge that a surface coming out of step 1 above would be closer to your subjects than the available PALS-B12 surfaces. But then your results would be less comparable to other studies than ones that mapped to these standard average fiducial surfaces. You see the trade-offs? Honestly, I don't think it's worth the effort, but I encourage my colleagues to speak up if they disagree. > Please correct me if I'm wrong. Thank you again, > > Bruno _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
