A magnetic resonance imaging (MRI) system (100) includes a memory (134) for storing machine executable instructions (140) and magnetic resonance fingerprinting (MRF) pulse sequence commands (142) which cause the MRI system to acquire MRF magnetic resonance data (144) according to an MRF protocol. The pulse sequence commands are configured for acquiring the MRF magnetic resonance data in two-dimensional slices (410, 412, 414, 416, 418, 420), having a slice selection direction. A train of pulse sequence repetitions includes a sampling event where the MRF data is repeatedly sampled. Execution of the machine executable instructions causes a processor to control the MRI system to: acquire (200) the MRF magnetic resonance data; construct (202) a series (148) of at least one magnetic resonance parameter value for each voxel of the two dimensional slices; and calculate (204) a composition (502, 504, 506, 508) of each of a set of predetermined substances within two or more sub-voxels (306, 308) for each voxel of the two dimensional slices using a sub-voxel magnetic resonance fingerprinting dictionary (150) for each of the two or more sub-voxels and the series of the at least one magnetic resonance parameter value. Each voxel in the slice selection direction is divided into two or more sub-voxels.