On 11/30/2006 08:34 AM, Mateus Joffily wrote:
Hi,

I have concluded the spherical registration of one individual surface into PALS-B12. Three spec files have been created:

(1) Human.Isa.R.spec (original spec file);
(2) deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec;
(3) deformed_Human.Isa.R.spec;

Could you, please, precise me differences among those three specs and for what purpose should I use each one? Although the names seem to be informative, when I compare the surfaces linked to each one, they look very similar, if not the same.
1) The original is what you created during segmentation, flattening, etc.
2) The deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec should be in your individual's surface directory. The dataset you downloaded is a stripped down version that contains no "goodies" (e.g., PALS border and paints, which you cite below). To get such "goodies" to automagically deform to your subjects' directories when you run registration, put the goodies in the atlas target directory and add them to your target registration spec (i.e., Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec). The one you currently have offers little, since it's designed more for the individual -> atlas direction (e.g., getting a bunch of depth or fMRI maps on the PALS mesh). But in your case, you care more about atlas -> individual. 3) The deformed_Human.Isa.R.spec is in your atlas target directory. Other than sanity checking the deformed fiducial, I don't personally use this spec file much. (And even when sanity checking, I use a SANITY_CHECK.spec that includes ALL my deformed fiducials and a single PALS closed topo.) More typically, you're interested in a particular file type -- e.g., deformed surface shape for sulcal depth; deformed metric for fMRI; deformed fiducial coord file for average fiducials. One typically concatenates all the deformed shape/metric into composite files and does group statistics on them.

In the next step, I would like to project PALS_B12 atlas (borders and paints) into the non-deformed individual surface. Could you, please, point me the documentation that explains how to do that, and how do I use the deformation map files?
The hard part is figuring out exactly which "goodies" (e.g., PALS paint, border, metric) you want deformed. Search for them in sumsdb.wustl.edu, or more likely find them in existing tutorials or datasets from figures in published papers that cite sumsdb links. You may find that the goodies in the visualization specs off the landmarks page meet your needs. If so, copy the appropriate paint, areacolor, border, bordercolor, metric, and/or palette files to your atlas target directory. Then add them to your atlas target spec. Then either re-run any registrations, or use Surface: Deformation: apply deformation map to apply the map in your individual's surface directory to the files in your atlas target directory.

Thanks again for your help.

Mateus
--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

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