Powell, Elizabeth;
Schneider, Torben;
Battiston, Marco;
Grussu, Francesco;
Toosy, Ahmed;
Clayden, Jonathan D;
Wheeler-Kingshott, Claudia AM Gandini;
(2022)
SENSE EPI reconstruction with 2D phase error correction and channel-wise noise removal.
Magnetic Resonance in Medicine
10.1002/mrm.29349.
(In press).
Preview |
PDF
Magnetic Resonance in Med - 2022 - Powell - SENSE EPI reconstruction.pdf - Published Version Download (6MB) | Preview |
Abstract
PURPOSE: To develop a robust reconstruction pipeline for EPI data that enables 2D Nyquist phase error correction using sensitivity encoding without incurring major noise artifacts in low SNR data. METHODS: SENSE with 2D phase error correction (PEC-SENSE) was combined with channel-wise noise removal using Marcenko-Pastur principal component analysis (MPPCA) to simultaneously eliminate Nyquist ghost artifacts in EPI data and mitigate the noise amplification associated with phase correction using parallel imaging. The proposed pipeline (coined SPECTRE) was validated in phantom DW-EPI data using the accuracy and precision of diffusion metrics; ground truth values were obtained from data acquired with a spin echo readout. Results from the SPECTRE pipeline were compared against PEC-SENSE reconstructions with three alternate denoising strategies: (i) no denoising; (ii) denoising of magnitude data after image formation; (iii) denoising of complex data after image formation. SPECTRE was then tested using high b $$ b $$ -value (i.e., low SNR) diffusion data (up to b = 3000 $$ b=3000 $$ s/mm 2 $$ {}^2 $$ ) in four healthy subjects. RESULTS: Noise amplification associated with phase error correction incurred a 23% bias in phantom mean diffusivity (MD) measurements. Phantom MD estimates using the SPECTRE pipeline were within 8% of the ground truth value. In healthy volunteers, the SPECTRE pipeline visibly corrected Nyquist ghost artifacts and reduced associated noise amplification in high b $$ b $$ -value data. CONCLUSION: The proposed reconstruction pipeline is effective in correcting low SNR data, and improves the accuracy and precision of derived diffusion metrics.
| Type: | Article |
|---|---|
| Title: | SENSE EPI reconstruction with 2D phase error correction and channel-wise noise removal |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1002/mrm.29349 |
| Publisher version: | https://doi.org/10.1002/mrm.29349 |
| Language: | English |
| Additional information: | © 2022 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | EPI, Nyquist ghost, SENSE, denoising, diffusion |
| UCL classification: | UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Neuroinflammation UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Med Phys and Biomedical Eng UCL > Provost and Vice Provost Offices > UCL BEAMS |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10152853 |
Archive Staff Only
 |
View Item |
