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= Using Your Data in Caret =

Caret reads a variety of data formats including files produced by other brain mapping software packages.  Visit the NITRC (Neuroimaging Informatics Tools and Resource Clearinghouse) [http://www.nitrc.org/  website] to learn about other neuroimaging software. 

== Anatomical Volume ==

If you have an anatomical volume (T1-weighted) of a human or monkey, you can use Caret to perform segmentation, that is, reconstruct the cortex into a surface model.  For more information, examine the Segmentation, Flattening, and Registration tutorial on the Documentation page.

== Contours/Sections ==

Caret is able to reconstruct a surface from countours.  Some files produced by MD Plot and Neurolucida can be read by Caret.  In addition, if you have images of sections, the images can be loaded into Caret and contours may then be drawn using the images.  See the Contours and Sections tutorial on the Documentation page.

== Functional Volume ==

If you have a functional volume, you can map the functional volume to a surface.  

If the functional data is of an individual, you will also need to generate a surface model for that individual and then map the functional volume to that individual's surface.  

If your functional volume contains group results, you can map the functional volume to the PALS.  The functional volume must be in one of the stereotaxic spaces supported by  Caret.  Available stereotaxic spaces include 711-2*, AFNI, FLIRT, MRITOTAL, SPM2, SPM95, SPM96, and SPM99 (others may have been added since this document was last updated).

== Foci ==

If you have a table of activations listing their stereotaxic coordinates, these coordinates can be entered into Caret using the PALS atlas.  For each coordinate entered, Caret will place a symbol at that location.  Each focus can be linked to a study by the study's PubMed ID.  

== Foci Database ==

The foci database contains over 20,000 foci from various journals including the Journal of Neuroscience.

== Surfaces ==

Caret can read surfaces produced by Brain Voyager and Free Surfer.  In addition, Caret is able to read surfaces from BYU, STL, and VTK files.