The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions which could not previously be answered and, as such, has become an important research area in its own right.In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data . The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL).

Perinatal stroke causes lifelong disability, particularly hemiparetic cerebral palsy. Arterial ischemic strokes (AIS) are large, cortical, and subcortical injuries acquired near birth due to acute occlusion of the middle cerebral artery. Periventricular venous infarctions (PVI) are smaller, subcortical strokes acquired prior to 34 weeks gestation involving injury to the periventricular white matter. Both stroke types can damage motor pathways, thus, we investigated resulting alterations in functional motor networks and probed function. We measured blood oxygen level dependent (BOLD) fluctuations at rest in 38 participants [10 arterial patients (age = 14.7 AE 4.1 years), 10 venous patients (age = 13.5 AE 3.7 years), and 18 typically developing controls (TDCs) (age = 15.3 AE 5.1 years)] and explored strength and laterality of functional connectivity in the motor network. Inclusion criteria included MRI-confirmed, unilateral perinatal stroke, symptomatic hemiparetic cerebral palsy, and 6-19 years old at time of imaging. Seed-based functional connectivity analyses measured temporal correlations in BOLD response over the whole brain using primary motor cortices as seeds. Laterality indices based on mean z-scores in lesioned and nonlesioned hemispheres explored laterality. In AIS patients, significant differences in both strength and laterality of motor network connections were observed compared with TDCs. In PVI patients, motor networks largely resembled those of healthy controls, albeit slightly weaker and asymmetric, despite subcortical damage and hemiparesis.Functional connectivity strengths were not related to motor outcome scores for either stroke group.This study serves as a foundation to better understand how resting-state fMRI can assess motor functional connectivity and potentially be applied to explore mechanisms of interventional therapies after perinatal stroke. K E Y W O R D Sperinatal stroke, functional connectivity, motor networks, resting-state fMRI, cerebral palsy, pediatric