Hello everyone,

I'm working on segmenting a NIfTI image using MRIcron, and I've encountered a challenge. My image is an RGB image, consisting of three color channels. My goal is to perform the segmentation specifically on the green channel. However, it's crucial for my analysis to observe and compare the same region across the other two channels (red and blue) simultaneously.

To achieve this, I open all three channels of my image in MRIcron. Then, I begin the segmentation process on the green channel. My question is: how can I ensure that the regions I've marked for segmentation on the green channel are visible or highlighted when I switch to view the red and blue channels? I need to ensure that the exact areas segmented in the green channel are accurately reflected and can be compared in the other two channels.

Any guidance or tips on how to manage this within MRIcron or through another method would be greatly appreciated.

(I attached a pdf of what I explained= showing 3 color channel of my nifti image and the segmented red marks on the green channel image)

I would use MRIcroGL for this. Use Fill/Open to open your background channel, and File/AddOverlay to add your additional layers. In the Layers panel, you will see all your layers listed. You can click on the layer name to set properties (e.g. in the screenshot I have selected the `green` image and set its color scheme to `2green`). Note that each layer has a checkbox that toggles if it is visible (or drag the opacity slider for translucent). The Draw/DrawColor allows you to set your drawing color. Note you can toggle layers on or off to see the desired layer.