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DIPY is the paragon 3D/4D imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.