Resolution and b value dependent structural connectome in ex vivo mouse brain

Abstract

Diffusion magnetic resonance imaging has been widely used in both clinical and preclinical studies to characterize tissue microstructure and structural connectivity. The diffusion MRI protocol for the Human Connectome Project (HCP) has been developed and optimized to obtain high-quality, high-resolution diffusion MRI (dMRI) datasets. However, such efforts have not been fully explored in preclinical studies, especially for rodents. In this study, high quality dMRI datasets of mouse brains were acquired at 9.4T system from two vendors. In particular, we acquired a high-spatial resolution dMRI dataset (25 μm isotropic with 126 diffusion encoding directions), which we believe to be the highest spatial resolution yet obtained; and a high-angular resolution dMRI dataset (50 μm isotropic with 384 diffusion encoding directions), which we believe to be the highest angular resolution compared to the dMRI datasets at the microscopic resolution. We systematically investigated the effects of three important parameters that affect the final outcome of the connectome: b value (1000s/mm² to 8000 s/mm²), angular resolution (10 to 126), and spatial resolution (25 µm to 200 µm). The stability of tractography and connectome increase with the angular resolution, where more than 50 angles is necessary to achieve consistent results. The connectome and quantitative parameters derived from graph theory exhibit a linear relationship to the b value (R² > 0.99); a single-shell acquisition with b value of 3000 s/mm² shows comparable results to the multi-shell high angular resolution dataset. The dice coefficient decreases and both false positive rate and false negative rate gradually increase with coarser spatial resolution. Our study provides guidelines and foundations for exploration of tradeoffs among acquisition parameters for the structural connectome in ex vivo mouse brain.

Keywords: Connectome; Crossing fiber; Diffusion MRI; HARDI; High-resolution.

Fig. 1.

Representative DTI metrics (a) and DWIs (b) at different b values (0 – 8000 s/mm²). The white matter exhibited a higher FA value compared to gray matter, while the MD value showed the opposite trend. The signal intensity gradually decreased with higher b value, the image at b value of 8000 s/mm² still exhibits relatively good image quality. The image magnitudes are normalized to the b0 image intensity. The SNR values varies from 85 (without diffusion weighting) to 15 (b value of 8000 s/mm²).

Fig. 2.

The connectivity maps at different threshold (0.0001 – 0.2), where connections become sparser with higher threshold (a-d). The highest dice coefficient is found at b value of 3000 s/mm² with single-shell acquisition (e) regardless of the threshold (0.0001 – 0.2). The false negative ratio (FNR) gradually decreases with higher b value, while false positive ratio (FPR) gradually increases with b value (i, j). Both FPR and FNR are lower than 0.2 using with more than two shells (k, l).

Fig. 3.

The tract density imaging (TDI) at different b values, including hippocampus (Hc), primary motor cortex (M1), and corpus callosum (cc). Compared to the ground truth (TDI in red color), the false negative (FN) tracts are apparent at lower b value (green arrows), while more false positive (FP) tracts exist at higher b values (white arrows). The tracts at b value of 3000 s/mm² are visually comparable to the ground truth, although a few false positive (FP) and false negative (FN) tracts can still be observed. The tracts from multi-shell (2000, 3000, and 4000 s/mm²) acquisition also show good overlap with the ground truth (purple arrows).

Fig. 4.

Compared to the ground truth (GT), there are more false positive (FP) connections in isocortex and white matter at higher b value (8000 s/mm²), while the connectome becomes sparser at b value of 1000s/mm².

Fig. 5.

Multiple fiber ratio (MFR) mapping at different b values. The ground truth (GT) is the dataset with all the b values (1000 - 8000 s/mm², 384 DWIs). The MFR is extremely low at b value of 1000s/mm². The MFR gradually increases with b value and the MFR is close to 1 (1 means every voxel of the brain has crossing fibers) at b value of 8000 s/mm² (h, q). For the single-shell acquisition, the MFR at b value of 3000 s/mm² matches with the ground truth best (q). The MFR is more stable when more shells are added (r, s, t). Green color: single fiber; Blue color: Multiple fibers; Ob: olfactory bulb; cc: corpus callosum; fi: fimbria; Hc: hippocampus.

Fig. 6.

The b value dependent fiber orientation distributions. Different layers with distinct fiber orientations are demonstrated in hippocampus (a). Compared to the b value of 3000 s/mm² (b), the crossing fibers are dominated in the hippocampus at b value of 8000 s/mm² (d). Significant MFR ratio difference was observed at different b values (c). cc: corpus callosum; sr: stratum radiatum; slm: stratum lacunosum-moleculare; mo: molecular layer; sg: granule cell layer of the dentate gyrus; po: polymorphic layer of the dentate gyrus;.

Fig. 7.

The quantitative metrics from graph theory as a function of the b value. A linear relationship between Graph Theory and b value has been observed for all three parameters (R² > 0.99), including density, path length, and small-world. For single-shell acquisition, the quantitative values at b value of 3000 s/mm² match well with the GT (a-c, purple dots). For two-shell (1000 and 2000s/mm², 3000 and 4000 s/mm², 5000 and 6000 s/mm², 7000 and 8000 s/mm²) acquisition, the quantitative values at b value of 3000 and 4000 s/mm² show consistent results with the GT (d-f).

Fig. 8.

The angular-dependent brain structural connectome. The whole brain connectome becomes sparser at lower angular resolution (a-f). The false negative ratio (FNR) drops dramatically with more angles and becomes more stable when the angular resolution is higher than 50 (h). In contrast, the false positive ratio (FPR) remains at a low level (< 0.1) through all the angular resolutions. The quantitative parameters (small-world, global efficiency, and clustering coefficient, i) variations respect to the angular resolution is similar to the dice coefficient (g), where more dramatically change is seen when the angular resolution is lower than 50.

Fig. 9.

The tractography result of the right corpus callosum (a-d) and right hemisphere (e-h) at different angular resolution (DWIs of 10, 60, and 126). The interhemispheric connections (red and green arrows) and long-range connections (white arrows) are largely reduced at lower angular resolution. DWI: diffusion weighted imaging.

Fig. 10.

The effect of the spatial resolution on the brain connectome. The microstructure and fiber directions are better resolved in white matter (WM), molecular layer (ml), and granular layer (gl) at higher spatial resolution (a-d). The Dice Coefficient decreases with lower spatial resolution, while both false positive ratio (FPR) and false negative ratio (FNR) gradually increase with lower spatial resolution. The capability of resolving crossing fibers is also reduced with lower spatial resolution.

Fig. 11.

The overlap of the tracer projection density for 5 injection sites (green color) and tractography results (red color). The Dice coefficient varies from 0.2830 to 0.5871 at different injections sites.