Hi Reza,

The atlas target dataset you used was the right one, but it is a stripped down version that minimizes the number of files that get deformed from the atlas to the individual's directory. (Some people want to look at the atlas paint or border files on their individual's surface, so then you would need to put those files in the atlas target directory and add them to your atlas spec file; then, they would automatically deform to the individual's directory during registration.)

Since you want to visualize on the atlas target, there's no need to re-register; rather, just download one or more of these datasets:



There are quite a few other options/documents listed here:


You can move your deformed results to the extracted directory, or move the extracted files to your atlas target directory -- your choice. I tend to create separate right and left subdirectories under my atlas target directory, which has lots of files, but when I run registration I use the single parent atlas target directory.

Often, we want to do group analysis of functional (metric) or anatomical (surface_shape) data; in these cases, we create composite metric or depth files. This command line utility (caret_command -help-full) can be helpful:

     caret_command -metric-or-shape-composite
     caret_command -metric-or-shape-composite-named-column

If you're going to use the tools under Attributes: Metric and Surface Shape Statistical Operations, then the spec files above lack the distortion metrics and OPEN topo files included in these analysis datasets:

* Visualization/Analysis spec LEFT: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486316 * Visualization/Analysis spec RIGHT: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486393

Most of the tests can be run using the caret_command utility.


On 02/21/2007 01:25 AM, Reza Rajimehr wrote:
Dear caret-users,

I did the spherical registration of an individual human brain to the human
PALS atlas. I used the following dataset as the target atlas brain:


A new deformed .spec file has been generated. However, it has only one new
surface, which is a deformed sphere. I would like to visualize the
functional activities of the individual brain on the atlas brain (e.g. on
the atlas flat map). Should I download a more elaborate PALS dataset and
add them to the current directory? If so, should I redo the spherical
registration, or the new PALS surfaces (e.g. inflated, flattened, ...)
will be automatically linked to the deformed spherical surface that I
already have?


Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129


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