Open-source 4D Phase Contrast MRI pipeline slashes scan times by 7x
From 80 minutes to 11 — open-source MRI pipeline revolutionizes muscle strain analysis
A team led by Marta B. Maggioni and Francesco Santini has published an open-source, vendor-agnostic pipeline for 4D Phase Contrast MRI that dramatically accelerates muscle imaging. The pipeline combines a compressed sensing-accelerated sequence implemented in PyPulseq with BART-based reconstruction and strain analysis. A gradient probing sequence ensures correct velocity sign assignment across different scanner orientations and manufacturers — addressing a common pitfall in multi-vendor studies.
Validated on two Siemens 3T MRI systems (MAGNETOM Prisma and Vida Fit), the pipeline reduced scan times from 35 minutes to 5 minutes for forearm muscle (Flexor Digitorum Superficialis) and from 80 minutes to 11 minutes for thigh muscle (Vastus Lateralis) during NMES-induced contractions. Strain analysis produced sigmoid-fitted curves yielding peak strain, mean strain, and buildup rate. Thigh muscle strains were an order of magnitude higher than forearm strains (median peak 0.49 vs. 0.063). The fully open-source framework supports reproducible research and can be adopted by labs with any MRI vendor.
- Compressed sensing reduces forearm scan from 35 to 5 minutes and thigh scan from 80 to 11 minutes.
- Validated on two Siemens 3T systems (Prisma and Vida Fit) with NMES-induced contractions in forearm and thigh.
- Open-source pipeline integrates PyPulseq, BART, and gradient probing for vendor-agnostic velocity sign correction.
Why It Matters
Enables fast, standardized, and reproducible muscle strain imaging accessible to any research lab.