Neuropsychiatric copy number variants (CNVs) provide unique insights into the genetic basis of neuropsychiatric disorders. This study utilised a novel approach for characterising morphology of white-matter fibres and combines them with more traditional volumetric and microstructural indices of white-matter to study their relation to penetrance for psychopathology in a CNV cohort. Results show cingulum morphology is significantly affected by the presence of CNVs with high-penetrance for schizophrenia and developmental disorders. Additionally, volumetric interrelationships across several white-matter structures are also altered. In particular, the ratios of tract volumes across segments of the corpus callosum are altered. It is likely that both these effects stem from a single neurodevelopmental trajectory characteristic of neuropsychiatric CNVs.