ASL maps can mainly be analyzed using the same tools to analyze fMRI and VBM. Many ASL-specific toolboxes have been developed to assist in ASL analysis, such as BASIL (Bayesian inference for arterial spin labelling MRI), part of the FSL neuroimaging package and also Ze Wang's ASL toolbox (using MATLAB) to assist in the subtraction and averaging of the tagged/control pairs. A visual quality check is often needed to make sure that the perfusion map is valid (such as correct registration, or correct segmentation of non-cerebral materials such as the dura mater). A whole brain/voxel-wise approach can be analyzed by registering the ASL map into MNI space for group comparisons. A region of interest approach can be analyzed by registering the ASL map into a selected cluster, or an atlas, like a standard (such as the Harvard-Oxford Cortical atlas) or an individual atlas developed by software like FreeSurfer. The recommended procedure of ASL registration for voxel-wise analysis is to register the perfusion map to a gray matter segmentation of each individual in a non-rigid procedure.
Gray matter often requires more oxygenation and is the source of more brain activity compared to white matter. Therefore, gray matter CBF is often higher than white matter CBF. The single value of gray matter CBF is often isolated in order to give a broad overview of CBF differences. Gray matter and white matter CBF can be localized using atlases or Freesurfer.
ASL functional connectivity can be designed with parameters conducive to a long scan time. Studies have suggested that ASL complement resting state fMRI findings well but can differentiate between resting brain networks (such as the default mode network) less.