usc-mrel / sparsepret1_dce

Precontrast T1 mapping

Matlab Codes for Sparse Pre-Contrast T1 Mapping for High-Resolution Whole-Brain DCE-MRI

Magnetic Resonance Engineering Laboratory (MREL)
University of Southern California

Code Structure

Demo script

demo.m Main script demonstrating sparse T1 mapping using a 256x256x12 anatomically realistic brain tumor Digital Reference Object (DRO).

Folders

DRO DRO generation, including 3T-mimicking noise.
images DRO sample images, including: ground truth M0 and T1 maps, reconstructed M0 and T1 maps, fractional difference maps.
results DRO results storage.
brain tumor ROI-level brain tumor patient data (tumor only).
Utils Utility functions, e.g. Fourier transform.

Functions (under Utils)

spgr.m VFA images signal intensity computation.
genKspace.m VFA k-space signal computation.
addNoise.m Generate and add synthesized noise.
applyU.m Generate and apply sparse sampling pattern.
P_SEN.m Reconstruction function.
P2sig.m Compute cost function value and gradient.
argmin.m Solver function.

Relevant References

1. Bosca RJ, Jackson EF. Creating an anthropomorphic digital MR phantom - An extensible tool for comparing and evaluating quantitative imaging algorithms. Phys Med Biol. 2016;61(2):974-982. doi:10.1088/0031-9155/61/2/974
2. Bliesener Y, Lingala SG, Haldar JP, Nayak KS. Impact of (k,t) sampling on DCE MRI tracer kinetic parameter estimation in digital reference objects. Magn Reson Med. 2020;83(5):1625-1639. doi:10.1002/mrm.28024
3. Stanisz GJ, Odrobina EE, Pun J, et al. T1, T2 relaxation and magnetization transfer in tissue at 3T. Magn Reson Med. 2005;54(3):507-512. doi:10.1002/mrm.20605
4. Müller A, Jurcoane A, Kebir S, et al. Quantitative T1-mapping detects cloudy-enhancing tumor compartments predicting outcome of patients with glioblastoma. Cancer Med. 2017;6(1):89-99. doi:10.1002/cam4.966
5. Hattingen E, Müller A, Jurcoane A, et al. Value of quantitative magnetic resonance imaging T1-relaxometry in predicting contrast-enhancement in glioblastoma patients. Oncotarget. 2017;8(32):53542-53551. doi:10.18632/oncotarget.18612
6. Badve C, Yu A, Dastmalchian S, et al. MR fingerprinting of adult brain tumors: Initial experience. In: American Journal of Neuroradiology. Vol 38. American Society of Neuroradiology; 2017:492-499. doi:10.3174/ajnr.A5035
7. Lebel RM, Guo Y, Lingala SG, Frayne R, Nayak KS. Highly accelerated DCE imaging with integrated T1 mapping. In: ISMRM 25th Scientific Sessions. Honolulu; 2017:138. https://cds.ismrm.org/protected/17MPresentations/abstracts/0138.html. Accessed May 12, 2020.

Questions? Contact [email protected].