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Specific thalamic nuclei are implicated in healthy aging and age-related neurodegenerative diseases. However, few methods are available for robust automated segmentation of thalamic nuclei. The threefold aims of this study were to validate the use of a modified thalamic nuclei segmentation method on standard T1 MRI data, to apply this method to quantify age-related volume declines, and to test functional meaningfulness by predicting performance on motor testing. A modified version of THalamus Optimized Multi-Atlas Segmentation (THOMAS) generated 22 unilateral thalamic nuclei. For validation, we compared nuclear volumes obtained from THOMAS parcellation of white-matter-nulled (WMn) MRI data to T1 MRI data in 45 participants. To examine the effects of age/sex on thalamic nuclear volumes, T1 MRI available from a second data set of 121 men and 117 women, ages 20-86 years, were segmented using THOMAS. To test for functional ramifications, composite regions and constituent nuclei were correlated with Grooved Pegboard test scores. THOMAS on standard T1 data showed significant quantitative agreement with THOMAS from WMn data, especially for larger nuclei. Sex differences revealing larger volumes in men than women were accounted for by adjustment with supratentorial intracranial volume (sICV). Significant sICV-adjusted correlations between age and thalamic nuclear volumes were detected in 20 of the 22 unilateral nuclei and whole thalamus. Composite Posterior and Ventral regions and Ventral Anterior/Pulvinar nuclei correlated selectively with higher scores from the eye-hand coordination task. These results support the use of THOMAS for standard T1-weighted data as adequately robust for thalamic nuclear parcellation., (© 2022 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.)

Purpose: Thalamic nuclei are largely invisible in conventional MRI due to poor contrast. Thalamus Optimized Multi-Atlas Segmentation (THOMAS) provides automatic segmentation of 12 thalamic nuclei using white-matter-nulled (WMn) Magnetization Prepared Rapid Gradient Echo (MPRAGE) sequence at 7T, but increases overall scan duration. Routinely acquired, bias-corrected Magnetization Prepared 2 Rapid Gradient Echo (MP2RAGE) sequence yields superior tissue contrast and quantitative T1 maps. Application of THOMAS to MP2RAGE has been investigated in this study., Methods: Eight healthy volunteers and five pediatric-onset multiple sclerosis patients were recruited at Children's Hospital of Philadelphia and scanned at Siemens 7T with WMn-MPRAGE and multi-echo-MP2RAGE (ME-MP2RAGE) sequences. White-matter-nulled contrast was synthesized (MP2-SYN) from T 1 maps from ME-MP2RAGE sequence. Thalamic nuclei were segmented using THOMAS joint label fusion algorithm from WMn-MPRAGE and MP2-SYN datasets. THOMAS pipeline was modified to use majority voting to segment bias corrected T1-weighted uniform (MP2-UNI) images. Thalamic nuclei from MP2-SYN and MP2-UNI images were evaluated against corresponding nuclei obtained from WMn-MPRAGE images using dice coefficients, volume similarity indices (VSIs) and distance between centroids., Results: For MP2-SYN, dice > 0.85 and VSI > 0.95 was achieved for five larger nuclei and dice > 0.6 and VSI > 0.7 was achieved for seven smaller nuclei. The dice and VSI were slightly higher, whereas the distance between centroids were smaller for MP2-SYN compared to MP2-UNI, indicating improved performance using the MP2-SYN image., Conclusions: THOMAS algorithm can successfully segment thalamic nuclei in MP2RAGE images with essentially equivalent quality as WMn-MPRAGE, widening its applicability in studies focused on thalamic involvement in aging and disease., (© 2020 International Society for Magnetic Resonance in Medicine.)

Volumes of thalamic nuclei are differentially affected by disease-related processes including alcoholism and human immunodeficiency virus (HIV) infection. This MRI study included 41 individuals diagnosed with alcohol use disorders (AUD, 12 women), 17 individuals infected with HIV (eight women), and 49 healthy controls (24 women) aged 39 to 75 years. A specialized, high-resolution acquisition protocol enabled parcellation of five thalamic nuclei: anterior [anterior ventral (AV)], posterior [pulvinar (Pul)], medial [mediodorsal (MD)], and ventral [including ventral lateral posterior (VLp) and ventral posterior lateral (VPl)]. An omnibus mixed-model approach solving for volume considered the "fixed effects" of nuclei, diagnosis, and their interaction while covarying for hemisphere, sex, age, and supratentorial volume (svol). The volume by diagnosis interaction term was significant; the effects of hemisphere and sex were negligible. Follow-up mixed-model tests thus evaluated the combined (left + right) volume of each nucleus separately for effects of diagnosis while controlling for age and svol. Only the VLp showed diagnoses effects and was smaller in the AUD (p = .04) and HIV (p = .0003) groups relative to the control group. In the AUD group, chronic back pain (p = .008) and impaired deep tendon ankle reflex (p = .0005) were associated with smaller VLp volume. In the HIV group, lower CD4 nadir (p = .008) was associated with smaller VLp volume. These results suggest that the VLp is differentially sensitive to disease processes associated with AUD and HIV., (© 2019 The Authors. Human Brain Mapping published by Wiley Periodicals, Inc.)

Purpose: To enable robust, high spatio-temporal-resolution three-dimensional Cartesian MRI using a scheme incorporating a novel variable density random k-space sampling trajectory allowing flexible and retrospective selection of the temporal footprint with compressed sensing (CS)., Methods: A complementary Poisson-disc k-space sampling trajectory was designed to allow view sharing and varying combinations of reduced view sharing with CS from the same prospective acquisition. These schemes were used for two-point Dixon-based dynamic contrast-enhanced MRI (DCE-MRI) of the breast and abdomen. Results were validated in vivo with a novel approach using variable-flip-angle data, which was retrospectively accelerated using the same methods but offered a ground truth., Results: In breast DCE-MRI, the temporal footprint could be reduced 2.3-fold retrospectively without introducing noticeable artifacts, improving depiction of rapidly enhancing lesions. Further, experiments with variable-flip-angle data showed that reducing view sharing improved accuracy in reconstruction and T 1 mapping. In abdominal MRI, 2.3-fold and 3.6-fold reductions in temporal footprint allowed reduced motion artifacts., Conclusion: The complementary-Poisson-disc k-space sampling trajectory allowed a retrospective spatiotemporal resolution tradeoff using CS and view sharing, imparting robustness to motion and contrast enhancement. The technique was also validated using a novel approach of fully acquired variable-flip-angle acquisition. Magn Reson Med 77:1774-1785, 2017. © 2016 International Society for Magnetic Resonance in Medicine., (© 2016 International Society for Magnetic Resonance in Medicine.)

Purpose: To develop a three-dimensional (3D) balanced steady-state free-precession (bSSFP) two-point Dixon method with banding-artifact suppression to offer robust high-resolution 3D bright-fluid imaging., Methods: A complex sum reconstruction that combines phase-cycled bSSFP images acquired at specific echo times for robust fat/water separation without banding was investigated and compared with a magnitude-based method. Bloch simulations using both single-peak and multiple-peak fat models were performed to predict the performance of these methods for a wide range of echo times and repetition times. The quality and degree of fat/water separation was evaluated in both simulations and using in vivo imaging., Results: Simulations predicted that both effective banding-artifact suppression and substantial improvements in fat/water separation are possible at echo times that are different from conventional echo times, enabling improved spatial resolution. Comparisons between various echo times and repetition times in vivo validated the improved fat/water separation and effective banding-artifact removal predicted by the simulations., Conclusion: The proposed complex sum Dixon 3D bSSFP method is able to effectively separate fat and water at different sets of echo times, while removing banding-artifacts, providing a fast, high-resolution, T2 -like sequence without blurring., (© 2014 Wiley Periodicals, Inc.)

Purpose: To optimize the white-matter-nulled (WMn) Magnetization Prepared Rapid Gradient Echo (MP-RAGE) sequence at 7 Tesla (T), with comparisons to 3T., Methods: Optimal parameters for maximizing signal-to-noise ratio (SNR) efficiency were derived. The effect of flip angle and repetition time (TR) on image blurring was modeled using simulations and validated in vivo. A novel two-dimensional (2D) -centric radial fan beam (RFB) k-space segmentation scheme was used to shorten scan times and improve parallel imaging. Healthy subjects as well as patients with multiple sclerosis and tremor were scanned using the optimized protocols., Results: Inversion repetition times (TS) of 4.5 s and 6 s were found to yield the highest SNR efficiency for WMn MP-RAGE at 3T and 7T, respectively. Blurring was more sensitive to flip in WMn than in CSFn MP-RAGE and relatively insensitive to TR for both regimes. The 2D RFB scheme had 19% and 47% higher thalamic SNR and SNR efficiency than the 1D centric scheme for WMn MP-RAGE. Compared with 3T, SNR and SNR efficiency were higher for the 7T WMn regime by 56% and 41%, respectively. MS lesions in the cortex and thalamus as well as thalamic subnuclei in tremor patients were clearly delineated using WMn MP-RAGE., Conclusion: Optimization and new view ordering enabled MP-RAGE imaging with 0.8-1 mm(3) isotropic spatial resolution in scan times of 5 min with whole brain coverage., (© 2014 Wiley Periodicals, Inc.)

The Bloch-Siegert (B-S) B1 (+) mapping technique is a fast, phase-based method that is highly SAR limited especially at 7T, necessitating the use of long repetition times. Spiral and echo-planar readouts were incorporated in a gradient-echo based B-S sequence to reduce specific absoprtion rate (SAR) and improve its scan efficiency. A novel, numerically optimized 4 ms B-S off-resonant pulse at + 1960 Hz was used to increase sensitivity and further reduce SAR compared with the conventional 6 ms Fermi B-S pulse. Using echo-planar and spiral readouts, scan time reductions of 8-16 were achieved. By reducing the B-S pulse width by a factor of 1.5, SAR was reduced by a factor of 1.5 and overall sensitivity was increased by a factor of 1.33 due to the nearly halved resonance offset of the new B-S pulse. This was validated on phantoms and volunteers at 7 T., (Copyright © 2013 Wiley Periodicals, Inc.)