Manual Segmentation of Mouse Cerebellum

[Nick Cottam]

Greetings,

I am currently exploring ITK-SNAPs potential application as a volumetric measurement for brain regions in mice (specifically the cerebellum).

I am using T1W images (nifti files) and labelling the cerebellum, all other regions, and background, in order to generate a 3D rendering of the cerebellum. That way I can extract the volume measurement. But, my classification is having a hard time differentiating from other regions and the cerebellum. The ROI is darkening, and I do not know why.

So, my question comes in three parts. Has anyone used ITK-SNAP for something like this and does it work? If so, do you have any advice for me? If not, is anyone aware of other softwares that are practical for taking MRI data and extracting regional volumes?

Thanks,

Nick