[caret-users] Problem color assignment

[Donna Dierker]

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.

>  
> Thanks a lot
> /Alireza
> --- On *Fri, 9/26/08, Donna Dierker /<donna.dierker at sbcglobal.net>/* 
> wrote:
>
>     From: Donna Dierker
>     Subject: Re: [caret-users] Problem with caret 5.1
>     To: alireza_sal2000 at yahoo.com
>     Cc: caret-users at brainvis.wustl.edu
>     Date: Friday, September 26, 2008, 7:27 PM
>
>     Not as far as I know, but I haven't tried.  If John made that
>     enhancement, it would be in the change log (see caret page).
>
>     ----- Original Message ----
>     From: Alireza Salamy <alireza_sal2000 at yahoo.com>
>     To: Donna Dierker <donna.dierker at sbcglobal.net>
>     Cc: caret-users at brainvis.wustl.edu
>     Sent: Friday, September 26, 2008 8:21:43 AM
>     Subject: Re: [caret-users] Problem with caret 5.1
>
>     Hello,
>      
>     what about the latest version of caret(5.6)?can it be feeded by
>     Spm5.Img/hdr pair?
>
>     --- On *Fri, 9/26/08, Donna Dierker
>     /<donna.dierker at sbcglobal.net>/* wrote:
>
>         From: Donna Dierker
>         Subject: Re: [caret-users] Problem with caret 5.1
>         To: alireza_sal2000 at yahoo.com
>         Date: Friday, September 26, 2008, 3:57 PM
>
>         Hi Alireza,
>          
>         If you are feeding Caret a SPM5 .img/.hdr pair, rather than a
>         .nii volume, this could happen.  Caret does not yet read NIfTI
>         .img/.hdr pairs properly; however, if you write the volume as
>         .nii, you'll have better luck.
>          
>         Donna
>
>         ----- Original Message ----
>         From: Alireza Salamy <alireza_sal2000 at yahoo.com>
>         To: caret-users at brainvis.wustl.edu
>         Sent: Friday, September 26, 2008 3:51:40 AM
>         Subject: [caret-users] Problem with caret 5.1
>
>         Hello,
>          
>         I am a new user,so sorry if this question sounds stupid.
>         I have a problem with caret 5.1.It does not actually show  my
>         activation of any of the hemisphere.First I chose the spec
>         file and then I choose map functional volume to matrix and
>         then choose the selected metric by primary overlap option but
>         nothing appears on my brain.I use SPM5 to make the image
>         file.Could it be the reason of coordinate of SPM5(isn't it
>         supported by this version of caret5.1)?shall I use the latest
>         version?
>         Thanks in advance
>         /A
>
>
>
>
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