Optimizing the magnetization-prepared rapid gradient-echo (MP-RAGE) sequence

Abstract

The three-dimension (3D) magnetization-prepared rapid gradient-echo (MP-RAGE) sequence is one of the most popular sequences for structural brain imaging in clinical and research settings. The sequence captures high tissue contrast and provides high spatial resolution with whole brain coverage in a short scan time. In this paper, we first computed the optimal k-space sampling by optimizing the contrast of simulated images acquired with the MP-RAGE sequence at 3.0 Tesla using computer simulations. Because the software of our scanner has only limited settings for k-space sampling, we then determined the optimal k-space sampling for settings that can be realized on our scanner. Subsequently we optimized several major imaging parameters to maximize normal brain tissue contrasts under the optimal k-space sampling. The optimal parameters are flip angle of 12°, effective inversion time within 900 to 1100 ms, and delay time of 0 ms. In vivo experiments showed that the quality of images acquired with our optimal protocol was significantly higher than that of images obtained using recommended protocols in prior publications. The optimization of k-spacing sampling and imaging parameters significantly improved the quality and detection sensitivity of brain images acquired with MP-RAGE.

Figure 1. Simulated signal intensity of the CSF and GM-WM contrast for different temporal positions of the read-out RF pulse at different Tis.

Figure 2. Simulated contrast between the GM and WM as functions of TI for total number of readout RF pulses of 176, 156, and 132.

The interval time between readout RF pulses was set to 10.1; the flip angle was set to 12°.

Figure 3. Human brain images acquired with an interval time between readout RF pulses of 10.1°, effective inversion recovery time of 950 ms, total readout RF pulse of 176, and slice partial Fourier factors of 1 (a), and 6/8 (b).

Figure 4. In vivo brain images acquired using the MP-RAGE sequence with different effective inversion recovery times : 900 (a), 950 (b), 1020 (c) and 1100 (d) ms at a flip angle of 12°, an interval time between readout RF pulses of 10.1 ms, and slice partial Fourier of 6/8.

Figure 5. Relationships between simulated signal intensities of brain tissues (the GM, WM and CSF) and flip angle at an interval time between readout RF pulses of 10.1 ms (a) and relationships between simulated contrasts of brain tissues (WM-GM, and GM-CSF) and flip angle under the optimal k-space trajectory (b).

Figure 6. In vivo brain images acquired using the MP-RAGE sequence with different flip angles: 9° (a), 11° (b), 12° (c), and 14° (d) with τ//TR = 10.1/950/1950 ms.

Figure 7. Simulated signal intensities of the GM, WM and CSF at different delay times (TD) at with N = 132 (slice partial Fourier factors of 6/8).

Figure 8. In vivo brain images acquired using the MP-RAGE sequence with different delay times (TD): 0 (a), 50 (b), 100 (c), 200 and 400 (d) ms.

Figure 9. In vivo brain images acquired using the MP-RAGE sequence with different imaging parameters: our optimized parameters (a), FreeSurfer (b), Siemens default (c), and ADNI (d).

Figure 10. The noise distribution of in-RAGE sequence with different imaging parameters: our optimized parameters (a), FreeSurfer (b), Siemens default (c), and ADNI (d).

Figure 11. Coronal brain images acquired using the MP-RAGE sequence with our optimized parameters (a) and acquired with imaging parameters recommended by FreeSurfer (b).

(c) and (d) are k-space representations of the images in (a) and (b), respectively.

Figure 12. k-space SNR of the images acquired using the MP-RAGE sequence with our optimized parameters and the imaging parameters recommended by FreeSurfer.