Synopsis

Classical T2 mapping based on 2D multi-echo spin-echo sequences achieves only limited across-slice resolutions. For clinical use, acquisitions with high isotropic resolution are however desirable, resulting in clinically prohibitive scan times. To this end, we propose a 3D multi-echo gradient and spin echo sequence with CAIPIRINHA and an additional model-based acceleration for T2 estimation. The combination of these techniques allows for whole-brain T2 mapping with 1.6mm-isotropic resolution in 3:26 min. The proposed framework was tested both in phantom and in vivo experiments.

Introduction

Quantitative T2 mapping of the human brain is typically performed using a 2D multi-echo spin-echo (MESE) sequence¹. A mono-exponential decay is voxel-wise fitted to estimate T2 values from images acquired at different echo times (TEs). Interleaved slice sampling is commonly employed to obtain maps within clinically acceptable acquisition times (TA). However, the 2D nature of the MESE sequence and specific absorption rate restrictions of multi-slice acquisitions impede high-resolution isotropic images. Higher and isotropic resolutions could be achieved with 3D MESE acquisitions; however, as 3D prohibits techniques like interleaved slice sampling, TAs become very long.

Here, we investigate brain T2 mapping with an undersampled 3D multi-echo gradient and spin echo (GRASE) sequence² as an alternative. In the multi-echo GRASE, an echo-planar-imaging (EPI) readout centered on each spin echo is introduced to reduce the TA in comparison to the MESE sequence. Further acceleration combining CAIPIRINHA³ and model-based reconstruction⁴ is explored, enabling scan times of under four minutes for a 1.6mm-isotropic whole-brain T2 map. The results are compared to reference T2 values estimated from single-echo spin-echo (SE) acquisitions in both phantom and in vivo experiments.

Methods

A prototype 3D multi-echo GRASE sequence that supports parallel imaging in both phase-encoding directions was implemented. A separate FLASH scan was acquired as calibration data for the CAIPIRINHA kernels.

All acquisitions were performed at 3T (MAGNETOM Skyra, Siemens Healthcare, Erlangen, Germany) using a standard 64-channel head/neck coil. Fully sampled and CAIPIRINHA-accelerated (R$$$_y$$$xR$$$_z\!$$$^Δk_$$$z$$$ = 2x2¹) multi-echo GRASE data were acquired in a multi-purpose phantom (five compartments with different concentrations of MnCl₂$$$\cdot$$$4H₂O). After obtaining written informed consent, the CAIPIRINHA-undersampled multi-echo GRASE sequence was scanned in two healthy volunteers (male, 25 and 29 y/o). For both phantom and in vivo experiments, a series of single-slice single-echo SE sequence was acquired with different TEs to compute reference T2 maps by fitting a mono-exponential decay. Relevant sequence parameters are listed in Table 1.

T2 maps were estimated from the multi-echo GRASE data by fitting an extended-phase-graph (EPG) model that assumes only one water compartment^5,6. Previous work⁷ demonstrated that high acceleration of a 2D MESE sequences can be achieved by combining parallel imaging and model-based iterative reconstruction. Following this idea, a combination of CAIPIRINHA and a split algorithm for fast T2 mapping (SAFT)⁴ was explored. To that end, the CAIPIRINHA-accelerated acquisitions were retrospectively undersampled with a block sampling pattern⁸ for additional three- and five-fold acceleration. First, CAIPIRINHA kernels were used to fill the missing lines within each sampling block (Figure 1). Subsequently, T2 maps were estimated by minimizing the following cost function:

$$X,\,T2,\,M_0,\,B1=\underset{X,T2,M_0,B1}{\arg\min}\frac{1}{2}\mid\mid\!AX-Y\!\mid\mid_2^2+\alpha\mid\mid\!X-M_0\,\mathrm{EPG}(T2,B1)\!\mid\mid_2^2$$

where $$$A$$$ is the encoding matrix which incorporates coil sensitivities, Fourier transform, and the block-sampling pattern, $$$X$$$ is the current image estimate, $$$Y$$$ the undersampled k-space data, $$$M_0$$$ the initial magnetization, $$$B1$$$ the nominal flip-angle, and $$$\alpha$$$ a regularization parameter. The free variables are estimated by splitting the cost-function and solving it alternatingly⁴.

T2 values within manually drawn ROIs in the phantom and volunteers were plotted and compared with a two-tailed t-test.

Results

In the phantom experiment, a significant difference (p<0.0025 after Bonferroni’s correction) between reference T2 values and multi-echo GRASE-derived maps with different undersampling schemes was found only in the compartments with the shortest and longest T2 (Figure 2). Notably, the retrospective undersampling of the data and model-based reconstructions did not introduce further variability, except for the compartment with the highest T2.

Representative in vivo T2 maps are shown in Figure 3. Contrary to the phantom experiment, the comparison among manually segmented ROIs in the brain revealed a slight systematic overestimation of the T2 values derived from the multi-echo GRASE data (Figure 4). However, the different undersampling strategies result in similar T2 values.

Discussion

Experiments conducted both in phantom and in vivo proved the capability of the proposed method to deliver isotropic T2 maps within acceptable clinical acquisition time.

Agreement between T2 values derived from single-echo SE and multi-echo GRASE acquisitions was demonstrated in phantom experiments for the biologically relevant range, even with highly undersampled data.

In vivo data revealed a slight T2 overestimation in multi-echo GRASE-based reconstructions, which seems systematic. This requires further investigation; possible sources include iron deposition, magnetization transfer, or multiple T2 components⁹. As a next validation step, possible differences between retrospective and real undersampling should also be studied.

Conclusion

Acknowledgements

References

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