Novel MR image acquisition strategies have been investigated to elicit contrast within the thalamus, but direct visualization of individual thalamic nuclei remains a challenge because of their small size and the low intrinsic contrast between adjacent nuclei. We present a step-by-step specific optimization of the 3D MPRAGE pulse sequence at 7T to visualize the intra-thalamic nuclei. We first measured T1 values within different sub-regions of the thalamus at 7T in 5 individuals. We used these to perform simulations and sequential experimental measurements (n=17) to tune the parameters of the MPRAGE sequence. The optimal set of parameters was used to collect high-quality data in 6 additional volunteers. Delineation of thalamic nuclei was performed twice by one rater and MR-defined nuclei were compared to the classic Morel histological atlas. T1 values within the thalamus ranged from 1400ms to 1800ms for adjacent nuclei. Using these values for theoretical evaluations combined with in vivo measurements, we showed that a short inversion time (TI) close to the white matter null regime (TI=670ms) enhanced the contrast between the thalamus and the surrounding tissues, and best revealed intra-thalamic contrast. At this particular nulling regime, lengthening the time between successive inversion pulses (TS=6000ms) increased the thalamic signal and contrast and lengthening the α pulse train time (N*TR) further increased the thalamic signal. Finally, a low flip angle during the gradient echo acquisition (α=4°) was observed to mitigate the blur induced by the evolution of the magnetization along the α pulse train. This optimized set of parameters enabled the 3D delineation of 15 substructures in all 6 individuals; these substructures corresponded well with the known anatomical structures of the thalamus based on the classic Morel atlas. The mean Euclidean distance between the centers of mass of MR- and Morel atlas-defined nuclei was 2.67mm (±1.02mm). The reproducibility of the MR-defined nuclei was excellent with intraclass correlation coefficient measured at 0.997 and a mean Euclidean distance between corresponding centers of mass found at first versus second readings of 0.69mm (±0.38mm). This 7T strategy paves the way to better identification of thalamic nuclei for neurosurgical planning and investigation of regional changes in neurological disorders.
Keywords: 7T; AV; Anterior ventral nucleus; CM; CNR; COM; CSF; Center median nucleus; Center of mass; Cerebro-spinal fluid; Contrast-to-noise ratio; Delay time; GM; Gray matter; Habenular nucleus; Hb; ICC; Intraclass correlation coefficient; Inversion time; LD; LGN; Lateral dorsal nucleus; Lateral geniculate nucleus; MD; MGN; MPRAGE sequence; MTT; Magnetization-prepared rapidly-acquired gradient echo sequence; Mammillothalamic tract; Medial geniculate nucleus; Mediodorsal nucleus; Pul; Pulvinar; RN; ROI; Red nucleus; Region-of-interest; SNR; Shot interval time; Signal-to-noise ratio; Sth; Subthalamic nucleus; TD; TI; TS; Thalamic nuclei; Thalamus; Ultra high field; VA; VLa; VLp; VPL; Ventral anterior nucleus; Ventral lateral anterior nucleus; Ventral lateral posterior nucleus; Ventral posterior lateral nucleus; WM; White matter; White matter nulled MPRAGE.