In this chapter, we explore the complex process of creating and analyzing connectomes in brain tumor patients, highlighting both methodological challenges and potential solutions. Connectomes, comprehensive maps of the brain’s structural and functional network, are crucial for understanding the organization of the brain and are particularly relevant in neurosurgery, as tumors affect not only the brain’s network and structures but also its functions. The construction of these connectomes relies on neuroimaging techniques such as diffusion-weighted magnetic resonance imaging (dMRI) for structural connectivity and functional magnetic resonance imaging (fMRI) for functional connectivity. The integration of these methods forms a cohesive framework for analyzing the connectomes of brain tumor patients. We address specific methodological challenges faced in connectome creation due to tumor-induced anatomical shifts and disruptions, such as difficulties in tissue segmentation and atlas registration. Furthermore, we discuss advancements like the transition from diffusion tensor imaging (DTI) to constrained spherical deconvolution (CSD) for more accurate neural pathway depiction. Despite these challenges, we emphasize the vital role of connectomics in a broader neurosurgical context, underscoring the potential of this field to further enrich our understanding of brain tumor-related connectivity alterations and provide a perspective in relation to TMS.