Motion-compensated low-rank reconstruction for simultaneous structural and functional UTE lung MRI
Tan F, Zhu X, Chan M, Zapala MA, Vasanawala SS, Ong F, Lustig M, Larson PEZ. Motion-compensated low-rank reconstruction for simultaneous structural and functional UTE lung MRI. Magn Reson Med. 2023. doi: 10.1002/mrm.29703
Tested with Python 3.10.6:
- numpy (>=1.21)
- sigpy (tested ==0.1.16)
- antspyx
- h5py
- pydicom
- cupy
- numba
- tqdm
- scipy
# convert ute data when using the uwute sequence
# uses the output 'MRI_Raw.h5' of pcvipr_recon_binary created using -export_kdata flag
python convert_uwute_npy.py ${file_dir} ${file_dir}
# run xd reconstruction
python recon_xdgrasp_npy.py ${file_dir} --res_scale 1 --vent_flag 1
# run lor reconstruction
python recon_lrmoco_npy.py ${file_dir} --lambda_lr 0.05 --vent_flag 1 --mr_cflag 0
# run mocolor reconstruction
python recon_lrmoco_vent_npy.py ${file_dir} --lambda_lr 0.05 --vent_flag 1 --reg_flag 1
# export DICOMs
python dicom_from_npy.py ${file_dir} ${orig_dicom_dir}
# rm temp files
rm bcoord.npy bdcf.npy bksp.npy _M_mr.npy