I am having trouble developing method for lesion segmentation from ct scans

I am developing a pipeline to segment lesions from CT scans in human subjects, but I am a bit confused about all the software.

Essentially, the steps I have are create a lesion mask (ITK-SNAP), skull strip, normalize to MNI space, and then convert MNI space to anatomical atlas.

I am confused on the differences between SPM and FSL. They have both been used in the literature on CT scan segmentation. Additionally, the SPM clinical toolbox created by Chris Rorden is an option for CT scans, but I am not sure if I can use this SPM toolbox with the Julich atlas.

I would appreciate any resources or explanations. My goal is to acquire lesion location from CT scans.