[caret-users] Visualizing functional data normalized to SUIT

[John Harwell]

Janine,

The Display Control's metric functions are described at "http://brainmap.wustl.edu/caret/caret_help/dialogs/display_control_dialog.html#Metric 
".  Caret's color palette file is actually the AFNI color palette file  
and is described at "http://afni.nimh.nih.gov/pub/dist/doc/program_help/README.setup.html 
".

Color palettes are used for coloring metric data, functional volumes,  
and may be used for coloring surface shape data.  A color palette  
contains a series of number-color pairs with the numbers ranging from – 
1.0 to 1.0.  The palette’s –1.0 is mapped to the most negative metric  
value, the palette's 0.0 to the 0.0 metric value, and the palette’s  
1.0 to the most positive metric value (although a user may override  
this on the Display Control’s Metric page).  A special color named  
“none” may be specified in the palette and operates as a transparent  
color resulting in no metric coloring.

Caret includes a number of palettes by default.  Additional color  
palettes are created or existing palettes edited using the Attributes  
Menu->Palette->Edit Dialog.

For an example of metric color assignment, see the table in the  
attached image.  Assume that the selected metric column’s values range  
from –10.0 to 10.0.  In addition, assume that Auto Scale is selected  
so that the metric 10.0 value is mapped to 1.0 in the palette and the  
metric -10.0 value is mapped to -1.0 in the palette.

  
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-----------------------------------
John Harwell
john at brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Apr 21, 2008, at 10:43 AM, J D Bijsterbosch wrote:
>
> Dear CARET users,
>
> I would like to visualize functional MRI group results to a flattened
> cerebellar
> atlas. I have normalized my images using the SUIT cerebellar  
> template and would
> like to visualize this using CARET. The SUIT package provides a spec  
> file and I
> have attempted to visualize my results using 'map volume(s) to  
> surface(s)' in
> CARET. However, my results are not the same as they are in SPM5.
>
> I am unclear about the steps to be taken and the meaning of for  
> example the
> thresholding and color-coding in the final image. The tutorials and  
> quick
> guides are not very helpful as they only tell you what to click for  
> the
> standard case with provided data and do not explain the meaning of  
> each step.
>
> I hope someone can help clarify the steps in CARET so that I can  
> visualize my
> results successfully.
>
>
> Best wishes,
>
>
> Janine Bijsterbosch
>
>
> Academic Clinical Psychiatry
> University of Sheffield
> United Kingdom
>
> ----- End forwarded message -----
>
>
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