PulmonaryMRI / imoco_recon

iterative Motion Compensation (iMoCo) reconstruction for MRI. Includes both Matlab and Python implementations. reference doi 10.1002/mrm.27998

iMoCo reconstruction for MRI

Description: iterative Motion Compensation reconstruction methods

Reference

Zhu, X, Chan, M, Lustig, M, Johnson, KM, Larson, PEZ. Iterative motion-compensation reconstruction ultra-short TE (iMoCo UTE) for high-resolution free-breathing pulmonary MRI. Magn Reson Med. 2020; 83: 1208– 1221. https://doi.org/10.1002/mrm.27998

Code Information

Contents

• ./imoco : iMoCo reconstruction in Matlab.
• ./recon_clean : iMoCo reconstruction preparation, including coil calibration, motion resolved reconstruction, carried out by BART (https://github.com/mrirecon/bart.git).
• ./imoco_py : python based iMoCo reconstruction. Sigpy and ANTs are required.
• ./imoco_npy: python based iMoCo reconstruction. Sigpy and ANTs are required. Support numpy array as I/O.

python packages required

Tested with Python 3.10.6

• numpy
• cupy
• sigpy
• h5py
• pydicom
• antspyx
• numba
• tqdm
• scipy

Sample dataset

https://zenodo.org/record/3733776#.XoJlNC2ZPOQ

Support

NIH NHLBI R01HL136965

Principal Investigators: Peder Larson, PhD (UCSF), Kevin Johnson, PhD (U Wisconsin), Shreyas Vasanawala, MD, PhD (Stanford), Miki Lustig, PhD (UC Berkeley)