One of the major challenges in clinical neuroimaging is to detect quantitative signs of pathological evolution as early as possible in order to prevent disease progression, evalute therapeutic protocols or even better understand and model the normal history of a given neurological pathology. This presentation will give some illustrations of this challenge from two types of procedures: Arterial Spin Labeling and application of image analysis in Multiple Sclerosis. Many pathologies encompass brain alterations often not visible on conventional MRI sequences, especially in normal appearing brain tissues (NABT). MRI often has a low specificity for differentiating between possible pathological changes which could aid in discriminating between the different pathological stages or grades. The objective of medical image analysis procedures is to define new neuroimaging biomarkers to track the evolution of the pathology at different level. This presentation will illustrate this issue at the metabolic level as well as at the structural and morphological level.