Regularly incremented phase encoding – MR fingerprinting (RIPE-MRF) for enhanced motion artifact suppression in preclinical cartesian MR fingerprinting

Fig. S1. Schematic of MRF pulse sequence with TR and FA patterns. The top panel demonstrates the inversion preparation combined with variable flip angles and repetition times played out until FAn and TRn (n=1,024). The slice gradient is unbalanced resulting in the dephasing needed to perform FISP imaging. This pattern is repeated for all lines of k-space changing the acquired phase encoding line based on the method implemented (SC-MRF or RIPE-MRF; Fig. 1). For each TR the phase encoding is perfectly balanced allowing for an arbitrary phase encoding order to be applied.

Fig. S2. Workflow of in vivo MRF experiments. Shown is the experimental work flow for two animals (out of 5 total) representing the two possible experimental designs. Three mice were imaged using the protocol demonstrated in Mouse 1 and two mice were imaged using the protocol for Mouse 2. The high anesthesia session was performed first to evaluate motion suppression in the presence of lower respiration and heart rates. Within this session the scan order was alternated to average out any physiological changes over the course of the experiment. Then 3 to 4 weeks later the low anesthesia state was imaged to analyze higher respiration and heart rates with the same alternation of the scan order. Total imaging time for each MRF acquisition was 45 minutes with the total scanning session being 1.5 hours (RIPE-MRF and SC-MRF).

Fig. S3. Composite MRF images for both SC-MRF and RIPE-MRF. Top and bottom rows are the same images; the top row is windowed to show anatomy, the bottom row is windowed to show artifacts. These composite MRF images were generated by calculating the magnitude of the complex sum of the dynamic MRF images in the time dimension. For these images, temporally coherent signals add constructively resulting in high signal magnitude whereas temporally incoherent signals will add destructively giving lower magnitude. SC-MRF shows high signal magnitude from artifact in the image background compared to RIPE-MRF indicating an element of incoherence being added to the artifact in the time domain when using the RIPE-MRF method. Some residual pulsatility artifacts are seen in the RIPE-MRF. Additionally, RIPE-MRF images appear to have less blurring.

Fig. S4. Shown are representative composite MRF images and MRF-based T₁ and T₂ maps to illustrate how ROIs were selected. For ANR measurements on the composite images (left column) ROIs were chosen to cover the entire phase encoding direction for the respiration artifact (blue), pulsatility artifact (green), and overall artifact (red) to analyze a similar number of pixels for each animal. T₁ and T₂ ROIs (middle and right column, respectively) show the presence of ROIs for respiration artifact (blue) and pulsatility artifact (green). Pulsatility was chosen anterior to the aorta and respiration was chosen laterally from the area of pulsatility to get consistently selected ROIs between animals.

Fig. S5. Representative M₀ maps from in vivo SC-MRF and RIPE-MRF acquisitions. These maps correspond to the T₁ and T₂ maps seen in Figure 4. In this study, the MRF-based M₀ maps are estimated as a scale factor and are not matched like T₁ and T₂. RIPE-MRF maps show distinct reductions in motion artifacts in comparison to SC-MRF similar to the T₁ and T₂ maps shown in Figure 4.

Fig. S6. Phantom results from spin echo, SC-MRF, and RIPE-MRF. T₁ and T₂ maps show similar quantitative values between both MRF methods and reasonable agreement with spin echo. Error bars are shown as the standard deviation of the 5 mean T₁ and T₂ estimates obtained for each phantom in the in vitro repeatability study. MRF-based T₁ estimates are significantly higher than conventional MRI estimates while MRF-based T₂ estimates are under-estimated. The phantom results are more consistent between the two MRF methods. (*P < 0.05, **P < 0.01, ***P < 0.005, ****P < 0.0005).