[caret-users] RGB paint option

[David Van Essen]

Hi Alireza,

One more option to add to Donna's good summary.

You can use Attributes: Metric: Convert Metric to RGB Paint.  This  
brings up  a reasonably self-explanatory popup window that allows you  
to assign one metric columns to the 'R' channel, another to the 'G'  
channel, and a third to the 'B' channel.  Where there is overlap  
between metric column data, the colors will blend.
The results can be viewed and saved as an RGBpaint file.

David

On Sep 29, 2008, at 9:03 AM, Donna Dierker wrote:

> Hi Alireza,
>
> See inline replies below.
>
> Donna
>
> On 09/27/2008 10:00 AM, Alireza Salamy wrote:
>> Hello again,
>>
>> How it would be possible to assign different colors to primary and
>> secondary overlap for the matrix type?
>>
> I'm not sure what you mean by primary and secondary overlap.  The term
> "matrix type" also isn't clear in this context.
>
> But knowing the two ways you can map data in Caret might help:
>
> 1.  Map functional volume as metric:  In this case, the volume  
> typically
> has  scalar intensity values, representing functional activity or some
> other continuously varying metric.  In this case, the color mapping is
> controlled by a palette file.  Caret has several on-board palette  
> files,
> but you can also create your own palette file.  If you're familiar  
> with
> AFNI's palette files, the format is similar.
>
> 2.  Map volume as paint or Region of Interest (ROI):  In this case,  
> the
> intensities represent discrete, categorical data, like architectonic
> regions.  Here, color mapping is determined by the area color file,
> which maps "paint names" (e.g., Brodman.12) to RGB colors.  The  
> mapping
> between intensity values and "paint names" can be tricky (look up
> table), and is stored in volume headers.  Caret recognizes this  
> mapping
> only in WUNIL 4dfp files and AFNI volumes with the "LUT" tag  
> inserted in
> the .HEAD.
>> for example assign red to the Primary overlap and blue to the
>> secondary overlap?
>>
> Again, "primary and secondary overlap" are not clear to me in this
> context, but perhaps the above explanations of Caret mapping options
> might help clarify.
>> In addition,how one can demonstrate the exact brodman area of the
>> mapped activation
>> ?I know that one can click on the activation and then check the paint
>> on the pop-ed-up identify window,but is that a way to show the  
>> brodman
>> area on the image beside the activation?
>>
> First, I just want to make it clear that your volume needs to be in a
> supported stereotaxic space (e.g., avg152 or Talairach) in order to  
> take
> advantage of atlases that label Brodmann areas.
>
> Caret doesn't (yet) have the capability to insert the Brodmann label
> directly on the surface from the graphical user interface.  There is a
> command line utility "caret_command -image-insert-text" with usage  
> like so:
>
> caret_command -image-insert-text
>         <input-image-file-name>
>         <output-image-file-name>
>         <text-x-position>  <text-y-position>
>         <text-red> <text-green> <text-blue>
>         <text>
>
>         Place the text into an image at the specified location.
>         The origin is at the bottom left corner of the image.
>
>         The red, green, and blue color components for the text
>         range from 0 to 255.
>
> But you have to specify the x and y positions of the text.
>
>>
>>