Dataset Information

Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing.

ABSTRACT: Macaque monkeys are an important animal model where invasive investigations can lead to a better understanding of the cortical organization of primates including humans. However, the tools and methods for noninvasive image acquisition (e.g. MRI RF coils and pulse sequence protocols) and image data preprocessing have lagged behind those developed for humans. To resolve the structural and functional characteristics of the smaller macaque brain, high spatial, temporal, and angular resolutions combined with high signal-to-noise ratio are required to ensure good image quality. To address these challenges, we developed a macaque 24-channel receive coil for 3-T MRI with parallel imaging capabilities. This coil enables adaptation of the Human Connectome Project (HCP) image acquisition protocols to the in-vivo macaque brain. In addition, we adapted HCP preprocessing methods to the macaque brain, including spatial minimal preprocessing of structural, functional MRI (fMRI), and diffusion MRI (dMRI). The coil provides the necessary high signal-to-noise ratio and high efficiency in data acquisition, allowing four- and five-fold accelerations for dMRI and fMRI. Automated FreeSurfer segmentation of cortex, reconstruction of cortical surface, removal of artefacts and nuisance signals in fMRI, and distortion correction of dMRI all performed well, and the overall quality of basic neurobiological measures was comparable with those for the HCP. Analyses of functional connectivity in fMRI revealed high sensitivity as compared with those from publicly shared datasets. Tractography-based connectivity estimates correlated with tracer connectivity similarly to that achieved using ex-vivo dMRI. The resulting HCP-style in vivo macaque MRI data show considerable promise for analyzing cortical architecture and functional and structural connectivity using advanced methods that have previously only been available in studies of the human brain.

SUBMITTER: Autio JA

PROVIDER: S-EPMC7116593 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing.

Autio Joonas A JA Glasser Matthew F MF Ose Takayuki T Donahue Chad J CJ Bastiani Matteo M Ohno Masahiro M Kawabata Yoshihiko Y Urushibata Yuta Y Murata Katsutoshi K Nishigori Kantaro K Yamaguchi Masataka M Hori Yuki Y Yoshida Atsushi A Go Yasuhiro Y Coalson Timothy S TS Jbabdi Saad S Sotiropoulos Stamatios N SN Kennedy Henry H Smith Stephen S Van Essen David C DC Hayashi Takuya T

NeuroImage 20200408

Macaque monkeys are an important animal model where invasive investigations can lead to a better understanding of the cortical organization of primates including humans. However, the tools and methods for noninvasive image acquisition (e.g. MRI RF coils and pulse sequence protocols) and image data preprocessing have lagged behind those developed for humans. To resolve the structural and functional characteristics of the smaller macaque brain, high spatial, temporal, and angular resolutions combi ...[more]

PMID: 32276072

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Project description:BACKGROUND:Quantitative myocardial perfusion cardiac MRI can provide a fast and robust assessment of myocardial perfusion status for the noninvasive diagnosis of myocardial ischemia while being more objective than visual assessment. However, it currently has limited use in clinical practice due to the challenging postprocessing required, particularly the segmentation. PURPOSE:To evaluate the efficacy of an automated deep learning (DL) pipeline for image processing prior to quantitative analysis. STUDY TYPE:Retrospective. POPULATION:In all, 175 (350 MRI scans; 1050 image series) clinical patients under both rest and stress conditions (135/10/30 training/validation/test). FIELD STRENGTH/SEQUENCE:3.0T/2D multislice saturation recovery T1 -weighted gradient echo sequence. ASSESSMENT:Accuracy was assessed, as compared to the manual operator, through the mean square error of the distance between landmarks and the Dice similarity coefficient of the segmentation and bounding box detection. Quantitative perfusion maps obtained using the automated DL-based processing were compared to the results obtained with the manually processed images. STATISTICAL TESTS:Bland-Altman plots and intraclass correlation coefficient (ICC) were used to assess the myocardial blood flow (MBF) obtained using the automated DL pipeline, as compared to values obtained by a manual operator. RESULTS:The mean (SD) error in the detection of the time of peak signal enhancement in the left ventricle was 1.49 (1.4) timeframes. The mean (SD) Dice similarity coefficients for the bounding box and myocardial segmentation were 0.93 (0.03) and 0.80 (0.06), respectively. The mean (SD) error in the RV insertion point was 2.8 (1.8) mm. The Bland-Altman plots showed a bias of 2.6% of the mean MBF between the automated and manually processed MBF values on a per-myocardial segment basis. The ICC was 0.89, 95% confidence interval = [0.87, 0.90]. DATA CONCLUSION:We showed high accuracy, compared to manual processing, for the DL-based processing of myocardial perfusion data leading to quantitative values that are similar to those achieved with manual processing. LEVEL OF EVIDENCE:3 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2020;51:1689-1696.

Project description:PurposeTo develop an endovaginal MRI array that provides signal enhancement forward into the posterior parametrium and sideways into the vaginal wall, accelerating multiple-contrast detection of residual tumors that survive external beam radiation. The array's enclosure should form an obturator for cervical cancer brachytherapy, allowing integration with MRI-guided catheter placement, CT, and interstitial radiation dose delivery.MethodsThe endovaginal array consisted of forward-looking and sideways-looking components. The forward-looking element imaged the cervix and posterior endometrium, and the sideways-looking elements imaged the vaginal wall. Electromagnetic simulation was performed to optimize the geometry of a forward-looking coil placed on a conductive-metallic substrate, extending the forward penetration above the coil's tip. Thereafter, an endovaginal array with one forward-looking coil and four sideways-looking elements was constructed and tested at 1.5 Tesla in saline and gel phantoms, and three sexually mature swine. Each coil's tuning, matching, and decoupling were optimized theoretically, implemented with electronic circuits, and validated with network-analyzer measurements. The array enclosure emulates a conventional brachytherapy obturator, allowing use of the internal imaging array together with tandem coils and interstitial catheters, as well as use of the enclosure alone during CT and radiation delivery. To evaluate the receive magnetic field ( B1- ) spatial profile, the endovaginal array's specific absorption-rate (SAR) distribution was simulated inside a gel ASTM phantom to determine extreme heating locations in advance of a heating test. Heating tests were then performed during high SAR imaging in a gel phantom at the predetermined locations, testing compliance with MRI safety standards. To assess array imaging performance, signal-to-noise-ratios (SNR) were calculated in a saline phantom and in vivo. Swine images were acquired with the endovaginal array combined with the scanner's body and spine arrays.ResultsSimulated B1- profiles for the forward-looking lobe pattern, obtained while varying several geometric parameters, disclosed that a forward-looking coil placed on a metal-backed substrate could double the effective forward penetration from approximately 25 to ∼40 mm. An endovaginal array, enclosed in an obturator enclosure was then constructed, with all coils tuned, matched, and decoupled. The ASTM gel-phantom SAR test showed that peak local SAR was 1.2 W/kg in the forward-looking coil and 0.3 W/kg in the sideways-looking elements, well within ASTM/FDA/IEC guidelines. A 15-min 4 W/kg average SAR imaging experiment resulted in less than 2o C temperature increase, also within ASTM/FDA/IEC heating limits. In a saline phantom, the forward-looking coil and sideways-looking array's SNR was four to eight times, over a 20-30 mm field-of-view (FOV), and five to eight times, over a 15-25 mm FOV, relative to the spine array's SNR, respectively. In three sexually mature swine, the forward-looking coil provided a 5 + 0.2 SNR enhancement factor within the cervix and posterior endometrium, and the sideways-looking array provided a 4 + 0.2 SNR gain factor in the vaginal wall, relative to the Siemens spine array, demonstrating that the array could significantly reduce imaging time.ConclusionsHigher SNR gynecological imaging is supported by forward-looking and sideways-looking coils. A forward-looking endovaginal coil for cervix and parametrium imaging was built with optimized metal backing. Array placement within an obturator enhanced integration with the brachytherapy procedure and accelerated imaging for detecting postexternal-beam residual tumors.

Dataset Information

Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing.

Publications

Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing.

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