Hi Joern,
First, for the benefit of most caret-users members, we still haven't
"officially" released PALS_B12, but we're getting pretty darned close.
The 40+ page paper has been submitted to Neuroimage, but it hasn't yet
been reviewed. Harold Burton's lab found some blemishes affecting a few
nodes that resulted in what look like pock marks in a couple of places
on the inflated surface, so I need to regenerate the registrations to
the spaces other than 711-2C (e.g., SPM2, SPM99, FLIRT, MRITOTAL, and AFNI).
After I do so, then I plan to create the average fiducial surface for
each of the six "spaces" PALS_B12 supports, including the four that are
MNI space. If you have the Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM*coord
files in your CARET_HOME/data_files/fmri_mapping_files directory, then
you can use Caret:Surface:Create Average Surface using the corresponding
coord files for each hemisphere to create an average fiducial. The
blemishes are pretty minor and unlikely to have much affect on
multi-fiducial mapping (MFM). Since you typically map individual data
and register in "surface-land," I'm not sure whether you ever downloaded
advance copies of the PALS_B12 MFM surfaces.
Anyway, once you have the average fiducial for each hemisphere in the
MNI space of your choice, then you can load that fiducial in your
visualization spec, so that ID node gives you that coordinate, and/or
you can use scripts to do the lookup on the coord file. If you do the
latter, then you might need to convert the binary coord file to ASCII,
depending on your script/program.
As for coordinate systems, I don't think David prescribes a "preferred"
coordinate system; he just outlines several, leaving the selection up to
the researcher, since the optimal system(s) will depend on the study.
We very much intend for folks to continue reporting 3d coordinates in
spaces compatible with their existing tool suite (e.g., MNI152/305,
711-2*, and AFNI +tlrc), and we plan to provide those average fiducial
files soon (days or weeks -- not months).
For the cool type of studies you are doing, I'd think you'd want to
report in multiple coord systems -- e.g., not only MNI but also
lat/long, since you're doing your analyses on the sphere in "surface-land."
For the foci, you might use the appropriate fiducial to find the focus'
nearest node (or project to it). Then, the latlon file provides the
lookup from node to lat/long. There may be a way to provide a
triangulated lat/lon based on the nearest tile, but if you want
something like that, then I'll ref you to John Harwell, who is closing
in fast on releasing an alpha version of Caret with SureFit segmentation
(yes, including automatic error correction).
On an unrelated note, I'd like to remind users about your interesting
Caret Surface Statistics paper:
http://www.bme.jhu.edu/~jdiedric/download/caret/Caret_surface_statistics_020205.pdf
It's only 12 pages -- concise and well-written. It proposes applying
random field theory to analysis on the surface. We'd very much like to
hear what users think about it.
Donna
On 03/24/2005 07:08 AM, Jörn Diedrichsen wrote:
Hi all,
I am just wondering if there is a elegant way of going from a Node on
the new PALS surface to the average coordinate in MNI space (maybe
even with SD over the 12 individuals) ?
I used spherical alignment to align all my subjects to the PALS
surface. It would be already great if there was a easy (!) way of
going from a PALS coordinate to the volume-coordinate in each of the
individuals native space, I could easily go from there and calculate
the MNI coordinate.
By the way of coordinate systems: what will be the preferred way of
reporting center of activations on PALS? The coordinates on the flat
surface? Lat/Long coordinates? If latter, how can I calculate/display
Lat/Long coordinates for foci on PALS?
Best,
Joern
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