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.
