On 11/30/2006 08:34 AM, Mateus Joffily wrote:
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);
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 ->
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.
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.
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?
Thanks again for your help.
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)