Fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging: Toward robust and reproducible metabolite measurements in human brain

Abstract

Purpose: To implement a fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging (MRSI).

Methods: The PRESS selected volume and outer-volume suppression bands were predefined on the MNI152 standard template image. The template image was aligned to the subject T₁ -weighted image during a scan, and the resulting transformation was then applied to the predefined prescription. To evaluate the method, H-1 MRSI data were obtained in repeat scan sessions from 20 healthy volunteers. In each session, datasets were acquired twice without repositioning. The overlap ratio of the prescribed volume in the two sessions was calculated and the reproducibility of inter- and intrasession metabolite peak height and area ratios was measured by the coefficient of variation (CoV). The CoVs from intra- and intersession were compared by a paired t-test.

Results: The average overlap ratio of the automatically prescribed selection volumes between two sessions was 97.8%. The average voxel-based intersession CoVs were less than 0.124 and 0.163 for peak height and area ratios, respectively. Paired t-test showed no significant difference between the intra- and intersession CoVs.

Conclusion: The proposed method provides a time efficient method to prescribe 3D PRESS MRSI with reproducible imaging positioning and metabolite measurements. Magn Reson Med 79:636-642, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Keywords: MRSI; atlas-based; automated; prescription; reproducibility.

Figure 1

Summary of the steps required for the automatic MRSI prescription.

Figure 2

Intra-subject reproducibility of the placement of MRSI PRESS volume/OVS bands and the spectra in serial scans. (a) Predefined MRSI PRESS volume (yellow rectangular boxes) and OVS bands (green-shaded bands) overlaid on the MNI152 standard 1mm T1-weighted atlas image. The size of the volume box is 80mm in RL (R51 to L130 in the atlas space coordinates), 100mm in AP (A157 to P58) and 50mm in SI (S114 to I65). (b) & (c) The PRESS volume and OVS bands transformed to a subject space in the baseline and follow-up scans, respectively. Note the PRESS volume is overlaid on the T1-weighted images that have been resampled and aligned to the PRESS volume. (d) & (e) The transformed PRESS volume and OVS bands overlaid on the subject’s original baseline and follow-up T1-weighted images, respectively. In (a), (b) and (c) the 3 orthogonal background image slices were chosen such that they all transverse the center of the PRESS volume box. It can be seen that although the orientation of the subject’s head was different between its baseline and follow-up scans, the locations of both PRESS volumes and OVS bands from both scans were still matched, with a Dice overlap ratio of 0.977. Also from (d) &(e), it is clear that the triple oblique prescription of PRESS volume was achieved.

Figure 3

(a) and (b) The baseline and follow-up spectra in the green grid on the coronal slices in Figure 2(b) and (c), respectively. (c) Overlay of the follow-up spectra on the top of the baseline ones. Note all spectra were displayed with the same intensity range, but the SNR and line width of Cre were similar between the two scans (Baseline/follow-up SNR: 13.4/12.2; Baseline/follow-up line width: 6.8/6.6Hz).