Computational Pipeline in Clinical Connectomics.

Understanding the neural basis of cognitive deficits following brain injury requires methods that can move beyond focal lesion analysis to capture the distributed nature of brain networks. This chapter presents a practical, step-by-step protocol for indirect disconnection mapping, a method that estimates white matter tract disruption from structural imaging alone, without requiring diffusion-weighted scans. By leveraging normative tractography data, this approach provides a means to infer the network-level consequences of lesions in both MRI and CT datasets. The procedure integrates widely used neuroimaging tools (MRIcron, BCBtoolkit, FSL, and SPM12) and supports both group-level and single-case analyses, including voxelwise statistical testing and Bayesian inference. Illustrated with the CT and MRI imaging of a patient, the workflow enables researchers and clinicians to map cognitive symptoms to patterns of structural disconnection, offering a reproducible and anatomically grounded framework for investigating and predicting brain-behavior relationships in clinical populations.