MRD file for simulation

MRD file for simulation#

SNAKE relies on the .mrd file format to store the raw data from MRI experiments.

The .mrd file format is a standard for sharing raw data of MRI experiments. The format is based on the HDF5 file format, which is a widely used file format for scientific data. The .mrd file format is designed to store raw data from MRI experiments, including the raw k-space data, the acquisition parameters, and other relevant information [1] The format is designed to be flexible and extensible, allowing for the storage of a wide range of data types and structures.

SNAKE MRD file structure#

SNAKE leverages the flexibility of the .mrd file format to store all the information need to simulate (f)MRI experiments. This allows the simulation to be performed in parallel (and very fast).

The SNAKE MRD file structure is as follows:

  • header group: contains the metadata for the file, as well as serialized information for the simulation.

  • acquisition group: contains the raw k-space data and the acquisition parameters.

  • images group: contains the static information for the simulation (phantom, coil sensitivity maps, etc.).

  • waveforms group: contains the dynamic information for the simulation (motion, physiological noise, etc.).

Reading and writing MRD files#

SNAKE provides a set of functions to read and write MRD files in the snake.mrd_utils module, built on top of the ismrmrd library.

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