Hi Jason,Donna's email nicely laid out our lab's perspective on several important issues regarding cortical landmarks and registration. I will amplify on a few aspects here. The issues that arise in considering whether the precentral sulcus may be a useful landmark are linked to the nature of individual variability and the relationship between cortical function and cortical folding. We wrestle with these issues regularly. While we don't claim to have definitive answers we do think that it is important to promote a stronger dialog among individuals and groups interested in the issues.
The challenges regarding the precentral sulcus can indeed be illustrated by inspection of individual sulcal depth maps from the PALS_B12 atlas. This can be done by downloading the datasets and viewing in Caret, as Donna described, but it can also be done using WebCaret without downloading data, as shown below.
The attached figure (if it gets past the filter) makes several important points, using dorsal views of the first four cases (B1.R - B4.R) from the atlas. A precentral sulcus is discernible in all 4 cases. However, in Cases 2 and 3 (middle 2) there is a big gap between superior and inferior precentral sulci. Moreover, the individual maps differ markedly in how the precentral sulcus terminates on the medial side (blue arrows). You can make educated guesses as to how the landmarks should be drawn in each case in order to maximize the correspondence of geographical and/or functional domains, but in our view it is very difficult to establish clear and objective criteria that have a good chance at improving the alignment of functional subdivisions across individuals.
Similar to what Donna proposed, you might consider starting by drawing contours for the fundus of the precentral sulcus in a group of hemispheres from our original PALS_B12 dataset (e.g., the four cases below). These landmarks from individual hemispheres can then be registered to the PALS atlas without doing a complete new registration - by using the appropriate deformation_map file (accessible from SumsDB; we can provide more detailed advice on how to do apply the deformation). Once you have done this, you can inspect how variable the position of the precentral fundus is by the standard PALS_B12 registration (i.e., using the Core6 landmarks).
If, on closer review, you still suspect that imposing the precentral sulcus as an additional landmark would reduce individual variability in maps of fMRI data (or other spatial data), then it is worth doing a full-blown analysis using the approach Donna outlined. If you do go down this road, we definitely urge that you do the side-by-side comparisons of the outcome of Core6 vs Connolly7 landmarks. It won't be a whole lot of extra work, and it will be the only way to ascertain whether the extra landmark helps or hinders in terms of reducing overall variance. Without parallel evaluations of this type, it will be difficult for us and others to assess the relative merits of different landmark-selection options.
I remain curious as to what types of experimental data you are trying to analyze and why you think that the precentral landmark might be a useful one to add.
Hope this helps. David
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On Apr 7, 2006, at 2:52 PM, Donna Dierker wrote:
Hi Jason,Dr. Van Essen and I just discussed your question, and we'd like more information about what you're trying to do. Often, there are easier ways to accomplish goals than posters envision.But to answer your question directly, no -- there are no published materials for adapting the core6 landmarks. (We typically use more landmarks for nonhuman primates, for whom variability is much less of an issue. I often refer users to the old Caret 4.6 Tutorial Part II, tutorial 8, Register Flat Maps, because I think it's a useful reference -- even though we don't use the flat map registration as a method anymore.)In principle, it's possible to add landmarks. In general, you would need to do this for each of the 24 PALS_B12 hemispheres (12 left, 12 right):1. Identify the landmark on the fiducial surface.2. Draw the border (probably easiest on the PALS flat surface, using the deformed folding as a shape underlay; we don't believe a composite folding file is available in sumsdb, but we have them).3. Project the border.4. Load the PALS_B12 spherical surface, and save the border relative to that surface. 5. Average the resulting borders to create an average PreCes target border for each hemisphere; add this border to the Core6 landmarks to generate a new landmark set -- let's call it Connolly7.Before going down this path, we think you would benefit from a warm- up exercise that might help you understand why the PreCes is not a core seventh landmark; we believe its variability makes it difficult to establish correspondence across subjects. Even where you can establish clear guidelines that can be applied consistently, we think this landmark will add more variance -- not reduce it.To see this personally, download the PALS tutorial here: http://sumsdb.wustl.edu/sums/directory.do?id=6332260 Go to scene 6A, Case1.R sulcal depth, four configurations. Switch the D/C menu from Scene to Surface Shape.Looking just at the very inflated and flat maps, toggle among the deformed depth columns for each of the 12 PALS_B12 right hemispheres. On each depth map, locate the PreCes on both the flat and very inflated maps.Note that the fiducial for Case 1 is shown in Window 3; since there aren't preset scenes for each subject, you'll need to use File: Open Data File: Coord file and navigate to your CARET_HOME/ data_files/fmri_mapping_files directory to load fiducial coord files for the other PALS_B12 subjects. (For each hemisphere, there is a coord file for each of the six atlas spaces we support; for the purposes of this exercise, it doesn't matter which you choose, as long as you get the right case number and make sure it's a right hemisphere -- named like *.R.*.)Case 1 has a nicely defined PreCes, so it won't be a problem. But several of the other cases illustrate the nature of the correspondence problem with this landmark. For registration purposes, we believe this problem creates more problems than it solves.But if you decide to go ahead and add additional landmarks, then we recommend you register your data both ways: Using the Core6 and the Connolly7. Once you get your data segmented and flattened, running registration multiple ways is easy; just make sure you use a different deformation prefix (fourth tab on the registration menu) and/or atlas target directory. (I'd recommend separate atlas target spec files, if not separate directories.) This way, you can compare the two and see which results you prefer. You may find they both are helpful, but tell you different things. Having the Core6 results will give you a way to compare your results with those of other labs who have used the Core6 landmarks.Happy morphing! On 04/06/2006 01:02 PM, Jason D Connolly wrote:Dear Caret-users, Is there any information in the tutorials, manuals etc. that can instruct us as to how to go about adapting the core6 landmarks to use our own landmarks (in addition to the core6) for morphing to the PALS atlas? We hope to use the precentral sulcus as an additional registration landmark ... Many thanks, Jason. ------------------------------------------------------------Jason D. Connolly, PhD Center for Neural Science, New York University6 Washington Place Room 875, New York, NY 10003cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 http:// www.psych.nyu.edu/curtislab/people/jasonconnolly.html_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users-- Donna L. Dierker(Formerly Donna Hanlon; no change in marital status -- see http:// home.att.net/~donna.hanlon for details.)_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
