I am not familiar with Analyze, but an RGB color-valued image is just a 4D volume, with the fourth dimension being 3. For each voxel, you have a 3D unit vector that can be displayed either as a color (the vector coordinates become the R,G,B values) or as a vector. I cannot see what is the extra information you are looking for.

It is likely that Analyze stores a flag in the header of these maps. That being the case, it can read these flags from the header and recognize automatically whether a vector-valued file should be displayed as RGB. However, this would require header modification of the files of interest rather than changing the data.

On 14 Jun 2012, at 15:27, Andrew Bender wrote:

Stam,

Thank you for your response. Other software (e.g., the DTI module in Analyze) actually outputs color maps, rather than relying on a display function. So, what I'm asking is whether there is a way to use fslmaths to produce an equivalent image to the display function in fslview, or some other script that might achieve that. Given the comparably limited capabilities for ROI production in FSLview, and the utility of using color maps as accessory images for producing ROIs, this seems like an important question that others would be interested in as well.

thanks,
Andrew

On Jun 12, 2012, at 7:00 PM, FSL automatic digest system wrote:

From: Stamatios Sotiropoulos <[log in to unmask]>
Date: June 12, 2012 6:04:46 AM EDT
Subject: Re: DTI eigenvalue color maps using fslmaths?

Hi Andrew,

There is nothing special with these RGB-color coded images, it is just the way they are displayed. FSLview reads the vector components in each voxel and displays them as an RGB color. So, it is up to whether a software package offers this type of display, not on some special information stored in the image.

Cheers
Stam

On 11 Jun 2012, at 23:52, Andrew Bender wrote:

Dear FSL community,

Does anyone know of a way or have a script to use fslmaths to generate an eigenvalue color map, as would be produced in Fslview by loading the principal diffusion V1 modulated by FA for to produce an RGB image? I am interested in drawing ROIs using Analyze, but using the color map as a supplementary image.

Thanks.

-Andrew