Robust T1-weighted structural brain imaging and morphometry at 7T using MP2RAGE

Abstract

Purpose: To suppress the noise, by sacrificing some of the signal homogeneity for numerical stability, in uniform T1 weighted (T1w) images obtained with the magnetization prepared 2 rapid gradient echoes sequence (MP2RAGE) and to compare the clinical utility of these robust T1w images against the uniform T1w images.

Materials and methods: 8 healthy subjects (29.0 ± 4.1 years; 6 Male), who provided written consent, underwent two scan sessions within a 24 hour period on a 7T head-only scanner. The uniform and robust T1w image volumes were calculated inline on the scanner. Two experienced radiologists qualitatively rated the images for: general image quality; 7T specific artefacts; and, local structure definition. Voxel-based and volume-based morphometry packages were used to compare the segmentation quality between the uniform and robust images. Statistical differences were evaluated by using a positive sided Wilcoxon rank test.

Results: The robust image suppresses background noise inside and outside the skull. The inhomogeneity introduced was ranked as mild. The robust image was significantly ranked higher than the uniform image for both observers (observer 1/2, p-value = 0.0006/0.0004). In particular, an improved delineation of the pituitary gland, cerebellar lobes was observed in the robust versus uniform T1w image. The reproducibility of the segmentation results between repeat scans improved (p-value = 0.0004) from an average volumetric difference across structures of ≈ 6.6% to ≈ 2.4% for the uniform image and robust T1w image respectively.

Conclusions: The robust T1w image enables MP2RAGE to produce, clinically familiar T1w images, in addition to T1 maps, which can be readily used in uniform morphometry packages.

Figure 1. MPRAGE (A), uniform T1w (B) and robust T1w (C) MP2RAGE image volumes of a healthy volunteer (male, 31years); the windowing for each image was chosen according to the transverse images.

The ratio (D = C/B) of the robust T1w over uniform T1w image shows that the inhomogeneity introduced by including β. The gross changes in the uniform T1w value occur in regions of poor B1⁺ transmit (cerebellum) or B1⁻ receive (brain centre) field coverage which result in a low signal intensity relative to β. The contrast seen in these ratio images also indicates that the choice of imaging parameters also has an effect, with cerebrospinal fluid experiencing a greater change relative to adjacent white or gray matter.

Figure 2. A uniform T1w MP2RAGE image (A) of a healthy volunteer (male, 31years) versus three different robust T1w images calculated with increasing β: β/10 (B) β (C) and 10β (D).

β must be chosen so that adequate noise suppression occurs without introducing the significant signal intensity bias seen in D.

Figure 3. An example of the background removal that results from the pre-processing steps proposed in , large portions of non-brain tissue remain.

Figure 4. Zoomed examples comparing uniform and robust T1w MP2RAGE images from healthy volunteers showing the noise suppression inside the skull (A); improved delineation of the cerebella lobes (B), brain stem (C), pituitary gland (D) and the temporal lobe (E) through the removal of the background noise and compensation of the inversion artefact.

Figure 5. Examples of the segmentation results with SPM8 (A) and MorphoBox (B) using uniform and robust T1w MP2RAGE images of healthy volunteers.

The colours represent the probability map from SPM8 or the label map from MorphoBox: red  =  cerebrospinal fluid; blue  =  white matter; green  =  gray matter; and the other colours represent additional structures identified with MorphoBox. The arrows indicate areas of more consistent segmentation with the anatomy (1); missed structures (2); and, background noise misclassified as either gray or white matter (3).

Figure 6. Percentage differences between repeat scans of the segmentation results when utilizing the uniform and robust T1w image.

(Error bars  =  max/min).