[caret-users] Caret and SPM5

[John Harwell]

Hi Jay,

On Oct 27, 2007, at 9:06 PM, Jay Hegdé wrote:

> Hi,
>    I have been using Caret to map functional data from SPM5 in  
> *.nii format onto PALS surfaces.  It works without a hitch and I  
> must say that the results are quite spectacular!  I'm sure the  
> results would be even better when the Caret template for SPM5  
> becomes available (I'm currently using SPM2 templates).
>
>    I do have two questions, both having to do with the fact that I  
> need to map a relatively large number of nii files (>100) to the  
> same color scale.  (Essentially, I need to make a time-lapse movie  
> of the % response change values over the course of the scan.)
>      (1) Is there a way I can specify the properties of color scale  
> (e.g., min, max, stepsize)?  I need to map all my nii files using  
> the *same* color scale.
>

On the Metric:Settings page of the Display Control Dialog, is a  
section titled "Color Mapping".  When set to Auto Scale (the  
default), the most positive metric value of the selected metric  
column maps to the 1.0 value of the color palette and the most  
negative metric value maps to the -1.0 value of the color palette.   
The problem you with your scale is that as you change metric columns,  
the color shown for a specific metric value may vary as a result of  
the metric columns minimum and maximum values.

In your case, I think you want to set Color Mapping to User Scale.   
With user scale, you can choose the metric values that map to 1.0  
(Pos Max) and -1.0 (Neg Max) values of the color palette.  By using  
User Scale, you will get a consistent mapping of metric values to the  
color palette as you cycle through your 100+ metric columns.

>    (2) Is there a way of automating the surface mapping process  
> (other than using "caret_map_fmri" perhaps)?  For instance, is  
> there a way I can record my menu selections and button presses,  
> save it as script, edit it as needed and run it?

Caret does not have a method of saving and replaying GUI actions as a  
script.   The "caret_map_fmri" program, which was intended to map  
individual functional volumes to individual surfaces, will no longer  
be included in future releases of Caret.  However, its functionality  
now part of next release of "caret_command".  In addition,  
caret_command is also able to map group average functional volumes to  
the PALS atlas.  Writing a script that maps your functional volumes  
is probably the best approach.  If you need the new version of  
caret_command or assistance in writing a script, let us know.


>    Thank you very much and best regards,
>    Jay Hegdé
>    University of Minnesota
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-----------------------------------
John Harwell
john at brainmap.wustl.edu

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