MONAI versions before 1.6.0 contain a remote code execution vulnerability in the algo_from_pickle() function due to unsafe pickle.loads() deserialization in monai/auto3dseg/utils.py. Attackers can craft malicious pickle files that execute arbitrary system commands when deserialized by the vulnerable function.

MONAI before 1.6.0 is vulnerable to OS command injection in the nnUNetV2Runner component (monai.apps.nnunet.nnunetv2_runner). User-controlled values taken from the YAML configuration file (notably dataset_name_or_id) and from CLI/kwargs arguments are concatenated into a command string without quoting or validation and then passed to subprocess with shell=True, so shell metacharacters (e.g., ';' on Linux, '&' on Windows) are interpreted. If a victim loads and processes a crafted configuration file — for example by instantiating nnUNetV2Runner with the malicious YAML and invoking a training/validation job such as train_single_model() — arbitrary commands are executed with the privileges of the user running the job.

MONAI before 1.6.0 contains an unsafe deserialization vulnerability in the NumpyReader class that unconditionally uses numpy.load with allow_pickle=True when loading .npy and .npz files. Attackers can craft malicious .npy files with pickle payloads that execute arbitrary code when loaded through MONAI's standard data pipeline.