MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field

Abstract

The large spatial inhomogeneity in transmit B 1 field (B 1 + ) observable in human MR images at high static magnetic fields (B 0 ) severely impairs image quality. To overcome this effect in brain T 1 -weighted images, the MPRAGE sequence was modified to generate two different images at different inversion times, MP2RAGE. By combining the two images in a novel fashion, it was possible to create T 1 -weigthed images where the result image was free of proton density contrast, T 2 ⁎ contrast, reception bias field, and, to first order, transmit field inhomogeneity. MP2RAGE sequence parameters were optimized using Bloch equations to maximize contrast-to-noise ratio per unit of time between brain tissues and minimize the effect of B 1 + variations through space. Images of high anatomical quality and excellent brain tissue differentiation suitable for applications such as segmentation and voxel-based morphometry were obtained at 3 and 7 T. From such T 1 -weighted images, acquired within 12 min, high-resolution 3D T 1 maps were routinely calculated at 7 T with sub-millimeter voxel resolution (0.65-0.85 mm isotropic). T 1 maps were validated in phantom experiments. In humans, the T 1 values obtained at 7 T were 1.15 ± 0.06 s for white matter (WM) and 1.92 ± 0.16 s for grey matter (GM), in good agreement with literature values obtained at lower spatial resolution. At 3 T, where whole-brain acquisitions with 1 mm isotropic voxels were acquired in 8 min, the T 1 values obtained (0.81 ± 0.03 s for WM and 1.35 ± 0.05 for GM) were once again found to be in very good agreement with values in the literature. © 2009 Elsevier Inc. All rights reserved. IntroductionIn the past decade, the magnetization-prepared rapid gradient echo, MPRAGE (Mugler and Brookeman, 1990), sequence has become one of the most commonly used sequences to obtain T 1 -weighted anatomical images of the human brain, in particular at high magnetic field. MPRAGE images are routinely used as anatomical reference for fMRI or for brain tissue classification in voxel-based morphometry (Ashburner and Friston, 2000). However, at high static magnetic fields (≥ 3 T), the increased inhomogeneity of the transmit B 1 + and receive B 1 − fields creates intensity variations throughout the image (bias field). Bias fields not only render segmentation and quantitative analysis difficult but also severely affect image quality at ultra-high fields (≥7 T). The use of adiabatic pulses to perform the inversion in the MPRAGE is only partially able to mitigate the effects of inhomogeneous B 1 . A number of strategies have been proposed to minimize or to correct bias fields generated by the inhomogeneity of the B 1 fields. Most correction strategies aim at correcting the combined (transmit and receive) bias field via post-processing techniques. This can be done either by low-pass filtering (Cohen et al., 2000;Wald et al., 1995) or by fitting slowly varying functions such as Gaussians or low order polynomials (Styner et al., 2000). The result from these low pass filters or fits is then su...

Density‐weighted concentric circle trajectories for high resolution brain magnetic resonance spectroscopic imaging at 7T

“…A magnetization‐prepared 2 rapid acquisition gradient echoes 34 sequence was measured for anatomical reference with a nominal resolution of 0.9 × 0.9 × 1.1 mm 3 within 5 min. To achieve the intended flip angle of 45° for the MRSI measurements, a $B_1^{+}$‐map was acquired with a pre‐saturation turboFLASH‐based B 1 mapping sequence 35, 36.…”

The impact of correction on MP2RAGE cortical T1 and apparent cortical thickness at 7T

“…Recently, the MP2RAGE sequence gained popularity at UHF, due to its easy implementation and efficiency to map T 1 at a submillimeter scale without significantly sacrificing SNR (and CNR). The MP2RAGE sequence allows the acquisition of a quantitative T 1 map and T 1 w image within a reasonable (i.e., <10 min) time frame (Marques et al, 2010). Whereas the T 1 map can be directly used to quantify microstructural (e.g., myelin)‐related changes of the brain (Stuber et al, 2014), the T 1 w image can be readily processed by publicly available software, such as the widely used FreeSurfer, to obtain cortical thickness maps (Fischl & Dale, 2000).…”

“…For example, to remedy T 1 errors, Marques et al (2010) provided a set of sequence parameters that limits the ${\mathrm{normalB}}_1^{+}$‐dependence of the MP2RAGE sequence, while simultaneously attaining sufficient CNR per unit time for segmentation. However, residual ${\mathrm{normalB}}_1^{+}$ dependency may still persist even for optimized MP2RAGE sequence parameters, as it assumes a homogeneous ${\mathrm{normalB}}_1^{+}$ during T 1 quantification.…”

“…MRI data were acquired using a whole‐body 7T magnet (Siemens Healthineers, Erlangen, Germany) and a 32‐channel phased‐array head coil (Nova Medical, Wilmington, MA, USA). High resolution (0.7 mm isotropic nominal voxel size) whole‐brain quantitative T 1 images were obtained with the MP2RAGE (Marques et al, 2010) sequence, and the Sa2RAGE (Eggenschwiler et al, 2012) sequence was used to map ${\mathrm{normalB}}_1^{+}$ (2 mm isotropic nominal voxel size) across the brain. MP2RAGE data were acquired with TR/TE = 5,000/2.47 ms, TI 1 /TI 2  = 900/2,750 ms, α 1 /α 2  = 5°/3° and generalized autocalibrating partially parallel acquisitions (GRAPPA) factor = 3 in the phase‐encoding (PE) direction (anterior–posterior) with 24 references lines.…”

“…These include, for example, spoiled gradient echo approaches, as implemented in several methods (Deoni, Rutt, & Peters, 2003; Helms, Dathe, & Dechent, 2008) or variations of the MPRAGE sequence (Liu, Bock, & Silva, 2011; Marques, Khabipova, & Gruetter, 2010). Here, the Magnetization‐Prepared 2 Rapid Acquisition Gradient Echo (MP2RAGE) sequence has recently gained popularity in higher field strengths studies (Marques et al, 2010). It combines two gradient‐recalled echo (GRE) images acquired at different inversion times (i.e., a predominantly T 1 w GRE 1 and PDw GRE 2 ) to obtain a quantitative T 1 map, calculated based on the bias‐free T 1 w combination image, sequence parameters and a lookup table.…”