I've been using QuickNII followed by Visualign to register 2D brain slices and quantify fluorescence in specific atlas labels using a custom FIJI macro. It works fairly well with ABA_Mouse_CCFv3_2017_25um, but I am having a hang up with the atlas outputs. Visualign gives 2 registered atlas images for each 2D slice (*.nl.png and *.nl_rbw.png). The *.nl.png files has ABA RGB values but at a low level of anatomical granularity (e.g., the whole midbrain has the same RGB value, ad the thalamus only have 2 or 3 different RGB values). in contrast, the *.nl_rbw.png files depict higher levels of anatomical, allowing for fluorescence quantification of discreet subregions of the midbrain and thalamus needed for my work. however, a given region in the *.nl_rbw.png files have different RGB values across different registered brain stacks, making it cumbersome to automatically pull ROI details across many brains (I need to manually identify the RGB for each brain before grabbing ROI details. 

Thus, I want to have VisuAlign output one of the following: 1) ABA labels at higher level of granularity, or 2) assign intensity values to specific brain regions such that the label intensity for each ROI is the same across brains. Is there any way to accomplish this by swapping out or editing the install files, or some other route of action?

Thank you for your time!