Hi all,

I am brand new to CONN Toolbox, and I'm currently making my way through the documentation and tutorials. 

I have manually traced dentate nuclei in a group of patients with cerebellar ataxias, and I want to do a seed to voxel resting-state functional connectivity analysis in CONN.

I have a couple of questions that I haven't been able to figure out from the documentation. First, will CONN accept/allow ROI's in native space or do they have to be normalised to MNI space, before importing them? I am also contemplating whether a normalisation to SUIT space is required for accurate registration of the cerebellum. Would anyone have some tips on how the workflow would look like? For example, would I need to do a normalisation of my images to SUIT space first (which does a normalisation and segmentation of the cerebellum and then crops out the cerebellum from the rest of the brain), and then use those images as my functional images to do denoising, or would I be better off doing all my preprocessing first and then using CONN just for the extraction of my ROI time series and functional connectivity with the rest of the brain?

Thank you in advance,

Rebecca