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imoco_recon's Introduction

iMoCo reconstruction for MRI

Description: iterative Motion Compensation reconstruction methods

image

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 People

Contributors

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Watchers

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Forkers

phillistan16 zoonono jiahwcu njstewart-eju mcencini polaris-sheffield

imoco_recon's Issues

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?

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

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