Brain mapping and connectomics can probe networks that span the entire brain, producing a diverse range of outputs for probing specific clinically relevant questions. Potential for understanding the impact of focal lesions on brain function, cognition, and plasticity abounds, any one of which would likely yield more effective and safer neurosurgical strategies. However, the possibilities of advanced MRI and connectomics are somewhat under utilized in neurosurgery, arising from actual or perceived difficulties in either application or analysis. This review builds on previous work describing the theoretical attractions of connectomics to deliberate on the practical details of doing high quality connectomics studies in neurosurgery. Initially, the data and methods involved in deriving connectomic models will be considered, specifically for the purpose of determining the nature of inferences that can be made subsequently. Next, a selection of key analysis methods will be explored using practical examples that illustrate their effective implementation, and the insights that can be gleaned. Principles of study design will be introduced, including analysis tips and means for making efficient use of available resources. Finally, a review of best research practices for neuroimaging studies will be discussed, including principles of open access data sharing, study pre-registration, and methods for improving replicability. Ultimately, we hope the reader will be better placed to appraise the current connectomics studies in neurosurgery as well as empowered to develop their own high-quality studies, both of which are key steps in delivering the true potential of connectomics and advanced neuroimaging analyses in general.