Erratum: T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm

Abstract We present an ultrahigh resolution in vivo human brain magnetic resonance imaging (MRI) dataset. It consists of T1-weighted whole brain anatomical data acquired at 7 Tesla with a nominal isotropic resolution of 250 μm of a single young healthy Caucasian subject and was recorded using prospective motion correction. The raw data amounts to approximately 1.2 TB and was acquired in eight hours total scan time. The resolution of this dataset is far beyond any previously published in vivo structural whole brain dataset. Its potential use is to build an in vivo MR brain atlas. Methods for image reconstruction and image restoration can be improved as the raw data is made available. Pre-processing and segmentation procedures can possibly be enhanced for high magnetic field strength and ultrahigh resolution data. Furthermore, potential resolution induced changes in quantitative data analysis can be assessed, e.g., cortical thickness or volumetric measures, as high quality images with an isotropic resolution of 1 and 0.5 mm of the same subject are included in the repository as well.

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Whole-Brain High-Resolution Metabolite Mapping with 3D Compressed-Sensing-SENSE-LowRank 1H FID-MRSI

10.1101/2020.05.18.101618 ◽

2020 ◽

Author(s):

Antoine Klauser ◽

Paul Klauser ◽

Frédéric Grouiller ◽

Sebastien Courvoisier ◽

Francois Lazeyras

Keyword(s):

High Resolution ◽

Brain Regions ◽

Low Rank ◽

Acquisition Time ◽

Resonance Spectroscopy ◽

Brain Anatomy ◽

Reconstruction Technique ◽

Whole Brain ◽

Isotropic Resolution

There is a growing interest of the neuroscience community to map the distribution of brain metabolites in vivo. Magnetic resonance spectroscopy imaging (MRSI) is often limited by either a poor spatial resolution and/or a long acquisition time which severely limits its applications for clinical or research purposes. We developed a novel acquisition-reconstruction technique combining fast 1H-FID-MRSI sequence accelerated by random k-space undersampling and a low-rank and total-generalized variation (TGV) constrained model. This framework was applied to the brain of four healthy volunteers. Following 20 min acquisition, reconstruction and quantification, the resulting metabolic maps with a 5 mm isotropic resolution reflected the detailed neurochemical composition of all brain regions and revealed part of the underlying brain anatomy. Contrasts and features from the 3D metabolite distributions were in agreement with the literature and consistent across the four subjects. The successful combination of the 3D 1H-FID-MRSI with a constrained reconstruction enables the detailed mapping of metabolite concentrations at high-resolution in the whole brain and with an acquisition time that is compatible with clinical or research settings.

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The SIGMA rat brain templates and atlases for multimodal MRI data analysis and visualization

Nature Communications ◽

10.1038/s41467-019-13575-7 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

D. A. Barrière ◽

R. Magalhães ◽

A. Novais ◽

P. Marques ◽

E. Selingue ◽

...

Keyword(s):

Rat Brain ◽

Ex Vivo ◽

Brain Mri ◽

Brain Structures ◽

Isotropic Resolution ◽

Complete Set ◽

Multimodal Mri ◽

Preclinical Mri ◽

Neuroimaging Software

AbstractPreclinical imaging studies offer a unique access to the rat brain, allowing investigations that go beyond what is possible in human studies. Unfortunately, these techniques still suffer from a lack of dedicated and standardized neuroimaging tools, namely brain templates and descriptive atlases. Here, we present two rat brain MRI templates and their associated gray matter, white matter and cerebrospinal fluid probability maps, generated from ex vivo $${\mathrm{T}}_2^ \ast$$T2*-weighted images (90 µm isotropic resolution) and in vivo T2-weighted images (150 µm isotropic resolution). In association with these templates, we also provide both anatomical and functional 3D brain atlases, respectively derived from the merging of the Waxholm and Tohoku atlases, and analysis of resting-state functional MRI data. Finally, we propose a complete set of preclinical MRI reference resources, compatible with common neuroimaging software, for the investigation of rat brain structures and functions.

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In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution

Scientific Data ◽

10.1038/s41597-021-00904-z ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Fuyixue Wang ◽

Zijing Dong ◽

Qiyuan Tian ◽

Congyu Liao ◽

Qiuyun Fan ◽

...

Keyword(s):

Diffusion Mri ◽

Parallel Imaging ◽

Brain Structures ◽

Test Bed ◽

Whole Brain ◽

Isotropic Resolution ◽

Imaging Reconstruction ◽

Further Development ◽

Array Coil

AbstractWe present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy participant. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition method, and parallel imaging reconstruction with advanced ghost reduction algorithm. With its unprecedented resolution, SNR and image quality, we envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance the understanding of human brain structures and connectivity. This comprehensive dataset can also be used as a test bed for new modeling, sub-sampling strategies, denoising and processing algorithms, potentially providing a common testing platform for further development of in vivo high resolution dMRI techniques. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale along with field maps are also made available.

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In vivo human whole-brain Connectom diffusion MRI dataset at 760 μm isotropic resolution

10.1101/2020.10.05.327395 ◽

2020 ◽

Author(s):

Fuyixue Wang ◽

Zijing Dong ◽

Qiyuan Tian ◽

Congyu Liao ◽

Qiuyun Fan ◽

...

Keyword(s):

Diffusion Mri ◽

Parallel Imaging ◽

Brain Structures ◽

Test Bed ◽

Whole Brain ◽

Isotropic Resolution ◽

Imaging Reconstruction ◽

Further Development ◽

Array Coil

AbstractWe present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy subject. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition method, and parallel imaging reconstruction with advanced ghost reduction algorithm. With its unprecedented resolution, SNR and image quality, we envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance the understanding of human brain structures and connectivity. This comprehensive dataset can also be used as a test bed for new modeling, sub-sampling strategies, denoising and processing algorithms, potentially providing a common testing platform for further development of in vivo high resolution dMRI techniques. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale along with field maps are also made available.

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Whole-brain 3D MR fingerprinting brain imaging: clinical validation and feasibility to patients with meningioma

Magnetic Resonance Materials in Physics Biology and Medicine ◽

10.1007/s10334-021-00924-1 ◽

2021 ◽

Author(s):

Thomaz R. Mostardeiro ◽

Ananya Panda ◽

Robert J. Witte ◽

Norbert G. Campeau ◽

Kiaran P. McGee ◽

...

Keyword(s):

White Matter ◽

Statistical Significance ◽

Relaxation Times ◽

Brain Structures ◽

Centrum Semiovale ◽

In Vivo Evaluation ◽

Whole Brain ◽

Mean Values ◽

Caudate Head

Abstract Purpose MR fingerprinting (MRF) is a MR technique that allows assessment of tissue relaxation times. The purpose of this study is to evaluate the clinical application of this technique in patients with meningioma. Materials and methods A whole-brain 3D isotropic 1mm3 acquisition under a 3.0T field strength was used to obtain MRF T1 and T2-based relaxometry values in 4:38 s. The accuracy of values was quantified by scanning a quantitative MR relaxometry phantom. In vivo evaluation was performed by applying the sequence to 20 subjects with 25 meningiomas. Regions of interest included the meningioma, caudate head, centrum semiovale, contralateral white matter and thalamus. For both phantom and subjects, mean values of both T1 and T2 estimates were obtained. Statistical significance of differences in mean values between the meningioma and other brain structures was tested using a Friedman’s ANOVA test. Results MR fingerprinting phantom data demonstrated a linear relationship between measured and reference relaxometry estimates for both T1 (r2 = 0.99) and T2 (r2 = 0.97). MRF T1 relaxation times were longer in meningioma (mean ± SD 1429 ± 202 ms) compared to thalamus (mean ± SD 1054 ± 58 ms; p = 0.004), centrum semiovale (mean ± SD 825 ± 42 ms; p < 0.001) and contralateral white matter (mean ± SD 799 ± 40 ms; p < 0.001). MRF T2 relaxation times were longer for meningioma (mean ± SD 69 ± 27 ms) as compared to thalamus (mean ± SD 27 ± 3 ms; p < 0.001), caudate head (mean ± SD 39 ± 5 ms; p < 0.001) and contralateral white matter (mean ± SD 35 ± 4 ms; p < 0.001) Conclusions Phantom measurements indicate that the proposed 3D-MRF sequence relaxometry estimations are valid and reproducible. For in vivo, entire brain coverage was obtained in clinically feasible time and allows quantitative assessment of meningioma in clinical practice.

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Myelin densities in retinotopically defined dorsal visual areas of the macaque

Brain Structure and Function ◽

10.1007/s00429-021-02363-z ◽

2021 ◽

Author(s):

Xiaolian Li ◽

Qi Zhu ◽

Wim Vanduffel

Keyword(s):

Visual Cortex ◽

Visual Field ◽

Cortical Thickness ◽

New World Monkeys ◽

Isotropic Resolution ◽

Density Mapping ◽

Area V2 ◽

Visual Areas ◽

Density Results

AbstractThe visuotopic organization of dorsal visual cortex rostral to area V2 in primates has been a longstanding source of controversy. Using sub-millimeter phase-encoded retinotopic fMRI mapping, we recently provided evidence for a surprisingly similar visuotopic organization in dorsal visual cortex of macaques compared to previously published maps in New world monkeys (Zhu and Vanduffel, Proc Natl Acad Sci USA 116:2306–2311, 2019). Although individual quadrant representations could be robustly delineated in that study, their grouping into hemifield representations remains a major challenge. Here, we combined in-vivo high-resolution myelin density mapping based on MR imaging (400 µm isotropic resolution) with fine-grained retinotopic fMRI to quantitatively compare myelin densities across retinotopically defined visual areas in macaques. Complementing previously documented differences in populational receptive-field (pRF) size and visual field signs, myelin densities of both quadrants of the dorsolateral posterior area (DLP) and area V3A are significantly different compared to dorsal and ventral area V3. Moreover, no differences in myelin density were observed between the two matching quadrants belonging to areas DLP, V3A, V1, V2 and V4, respectively. This was not the case, however, for the dorsal and ventral quadrants of area V3, which showed significant differences in MR-defined myelin densities, corroborating evidence of previous myelin staining studies. Interestingly, the pRF sizes and visual field signs of both quadrant representations in V3 are not different. Although myelin density correlates with curvature and anticorrelates with cortical thickness when measured across the entire cortex, exactly as in humans, the myelin density results in the visual areas cannot be explained by variability in cortical thickness and curvature between these areas. The present myelin density results largely support our previous model to group the two quadrants of DLP and V3A, rather than grouping DLP- with V3v into a single area VLP, or V3d with V3A+ into DM.

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