recoMRD

This project is deprecated. The ongoing developments have been transferred to the recotwix project.

Scripts to read and reconstruct ismrmrd (mrd) format

There are a few jupyter notebooks in the example folder to demo how to use recoMRD. Testing MRD files can be downloaded from here.

Install

Dependecies

This program uses following (optional) tools. Compiled binaries are provided in the lib folder.

• Standalone brain extraction tool (BET2) for brain masking +
• SRNCP 3D phase unwrapping +

BART toolbox is used for some of coil combination methods (optional).

Class overview

Inheritance tree:

|--readMRD
    |-- recoMRD
        |-- recoMRD_B0
        |-- recoMRD_B1TFL
        |-- recoMRD_custom

Important class members

readMRD

kspace : n dimension data storing different scan types, e.g., kspace, navigator, feedback, auto calibration scan, etc. dim_size : length of fully sampled acquired data in each dimension (no accelration, no partial fourier, no asymmetric echo, no ...?)
matrix_size : size of fully sampled 3D volume in k-space and image space
fov : FoV in k-space and image space
enc_minmax_ind : index of the first and the last sample/line for all encoding directions

in progress ...