MRD Tools

MRD includes useful tools for working with MRD streams.

These tools are available in the MRD conda package and in the MRD Docker image.

The source for each tool can be found in the cpp/mrd-tools subdirectory of the MRD repository.

Generating a Phantom

To quickly generate a cartesian Shepp-Logan phantom (k-space data), use mrd_phantom.

Optionally specify the number of coils, matrix size, number of repetitions, and oversampling factor.

$ mrd_phantom -c 8 -m 256 -r 2 -s 2 > phantom.bin
# OR
$ mrd_phantom --coils 8 --matrix 256 --repetitions 2 --oversampling 2 > phantom2.bin

Stream Reconstruction

To reconstruct 2D images (such as a cartesian phantom generated using mrd_phantom), use mrd_stream_recon.

This tool reads an MRD stream of Acquisitions from stdin and writes the output MRD stream of Images to stdout.

$ cat phantom.bin | mrd_stream_recon > images.bin

Convert Images to PNG

To easily view Images in an MRD stream, use mrd_image_stream_to_png to convert them to PNG files.

This tool reads an MRD stream of Images from stdin and writes the output PNG files to disk.

$ cat images.bin | mrd_image_stream_to_png ./result
$ ls
result000000.png  result000001.png

ISMRMRD <-> MRD converter

To enable interoperability with the older ISMRMRD format, the MRD repository contains tools for roundtrip conversion between the two formats.

• mrd_to_ismrmrd: Convert a binary MRD stream (stdin) to an ISMRMRD stream (stdout)
• ismrmrd_to_mrd: Convert an ISMRMRD stream (stdin) to an MRD stream (stdout)

# Use ISMRMRD tools to generate a dataset and convert it to a stream
$ ismrmrd_generate_cartesian_shepp_logan -o phantom.h5
$ ismrmrd_hdf5_to_stream -i phantom.h5 --use-stdout > direct.bin

# This time, convert the ISMRMRD stream to MRD, then back again
$ ismrmrd_hdf5_to_stream -i phantom.h5 --use-stdout | ismrmrd_to_mrd | mrd_to_ismrmrd > roundtrip.bin

# The files are identical
$ diff direct.bin roundtrip.bin