Review of ISMRMRD

The ISMRM Raw Data (ISMRMRD) format originates from a subcommittee formed at the 2013 ISMRM Sedona, Arizona workshop on image reconstruction. ISMRMRD aims to meet the critical need for a vendor-neutral (non-proprietary) file format for MR research and development, especially in light of the widespread push for reproducible research across all disciplines of biomedical science. Potential users of the domain-specific ISMRMRD format may be skeptical of the underlying domain-independent Hierarchical Data Format (HDF5) format, but that should not be a concern. HDF5 comes from the National Center for Supercomputing Applications (NCSA). If you use a recent version of MATLAB, you are already using HDF5 when saving .MAT files from MATLAB. Support for loading HDF5, and hence ISMRMRD, is widespread with functions/modules in Python, MATLAB, C/C++, Java, Julia, etc. ISMRMRD-specific interfaces are available for MATLAB and Python. It is important to note that ISMRMRD files include creation dates for the file and objects within a file (as do all HDF5 files by default). This causes two ISMRMRD files containing the exact same data, but created at different times, to have a different checksum value. To accurately compare two ISMRMRD files, a utility such as h5diff should be used.

Currently, the ISMRMRD source code must be compiled, and there are instructions for Linux, Mac OS X, and Windows. This reviewer was able to compile ISMRMRD using the instructions provided for each platform. The set of compiled binaries include tools to simulate k-space for the Sheep-Logan phantom and to perform a basic Cartesian reconstruction. An important development since the establishment of the ISMRMRD file format is a set of open-source converters to transform vendor-specific raw data files from Bruker, GE, Philips or Siemens to ISMRMRD. An ISMRMRD data set is comprised of 2 sections:

  1. A flexible XML document that can contain an arbitrary number of fields and accommodate everything from simple values (b-values, etc.) to entire vendor protocols. 
  2. A raw data section containing all the acquired data in the MR experiment. Each data item is preceded by a C-struct with encoding numbers, etc. followed by a receive channel header and data for each acquired channel. 

ISMRMRD can also store reconstructed spatial domain images. More details of the ISMRM raw data format appear in a 2016 peer reviewed publication in the journal Magnetic Resonance in Medicine (http://dx.doi.org/10.1002/mrm.26089). The manuscript describes the design strategy, general specifications and some implementation details of the file format. Table 1 in the paper is particularly useful because it shows how dimension labels from different vendors are mapped to the ISMRMRD labels. For example, the “echo” number label is mapped to the ISMRMRD label named "Contrast". The published paper includes examples from multiple vendors using Cartesian, spiral and EPI data sets. ISMRMRD supports storing arbitrary k-space coordinates making it very well suited for non-Cartesian applications.

In summary, the ISMRMRD file format has high potential to make a positive impact on the MR research community. The success of the format will undoubtedly be determined by how widespread its use becomes among MR researchers. If you believe in open and reproducible research, then you should strongly consider using ISMRMRD.
Reviewed April 2016