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)

imoco_recon's Issues

Convert to ANTsPy

Use the ANTs python API for the imoco_py
ANTsPy package
https://antspyx.readthedocs.io/en/latest/?badge=latest#
https://github.com/ANTsX/ANTsPy

pip install antspyx

replace code in imoco_py/sigpy_e/reg.py

How do I obtain raw data in .cfl format to use with this code?

Hi,

I was checking the code in this repo, and while I am somehow familiar with sigpy and the other libraries being used, I was hoping to find a way to convert raw data exported from the scanner (in my case a Siemens mMR, so files in twix format) to .cfl that I can then import and use with this code.

Do you have any suggestions about this?

Thank you!

Add online demo

Options:
Binder (would support Octave version)

Google CoLaboratory - python only

Add support for ISMRMRD format

Consider switching to ISMRMRD format instead of CFL for input data

Docker support and release

Add Docker support
New release when Docker support is tested

Missing components of Sample Dataset?

From user:
The matlab code is trying to load a “_mrL.cfl” and a “_maps.cfl” file which don’t seem to be part of the sample data. Are these somehow included in the “_imoco.cfl” file?