Dear Donna and David,

Thank you for the helpful comments and suggestions. I successfully
finished flattening of an individual human brain and its spherical
registration to the human PALS atlas, and the registration is perfect. Now
I want to start flattening of an individual monkey brain and its spherical
registration to the macaque F99UA1 atlas. Before starting this process, I
just wanted to make sure that I am using the correct (and the most
up-to-date) files. In particular, I would appreciate if you provide me
with the SumsDB links for the following files:

1) Macaque template cuts for flattening (border file and border color file).

2) Macaque landmarks for registration (border color file and border
projection file).

3) F99UA1 atlas for registration (.spec, .deform_map, and sphere.coord
files).

4) The complete F99UA1 atlas containing various .coord files (and other
Caret files) for surface visualization.


and a brief question about flattening: where is the location of "temporal
and frontal cuts" on the macaque cortex, and how can I draw them? (i.e.
where are the recommended start and end points for these cuts?)

Thanks,
Reza


> 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:
>
> PALS_B12.LEFT.STANDARD-SCENES.73730.spec
> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595803
>
> PALS_B12.RIGHT.STANDARD-SCENES.73730.spec
> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595827
>
> There are quite a few other options/documents listed here:
>
> CARET_TUTORIAL_SEPT-06
> http://sumsdb.wustl.edu/sums/directory.do?id=6585200
>
> 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.
>
> Donna
>
> 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:
>>
>> http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499
>>
>> 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?
>>
>> Thanks,
>> Reza
>>
>> ********************************
>> Reza Rajimehr, MD
>>
>> NMR Athinoula A. Martinos Center
>> Department of Radiology
>> Massachusetts General Hospital (MGH)
>> Building 149, 13th St.
>> Charlestown, MA 02129
>>
>> Email: [EMAIL PROTECTED]
>> ********************************
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users


********************************
Reza Rajimehr, MD

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

Email: [EMAIL PROTECTED]
********************************

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