SENSE EPI reconstruction with 2D phase error correction and channel‐wise noise removal

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 highb $$ b $$ ‐value (i.e., low SNR) diffusion data (up tob = 3000 $$ b=3000 $$  s/mm2$$ {}^2 $$ ) 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 highb $$ b $$ ‐value data. Conclusion The proposed reconstruction pipeline is effective in correcting low SNR data, and improves the accuracy and precision of derived diffusion metrics.