Systems and methods for analyzing perfusion-weighted medical imaging using deep neural networks are provided. In some aspects, a method includes receiving perfusion-weighted imaging data acquired from a subject using a magnetic resonance (“MR”) imaging system and modeling at least one voxel associated with the perfusion-weighted imaging data using a four-dimensional (“4D”) convolutional neural network. The method also includes extracting spatio-temporal features for each modeled voxel and estimating at least one perfusion parameter for each modeled voxel based on the extracted spatio-temporal features. The method further includes generating a report using the at least one perfusion parameter indicating perfusion in the subject.
