Paravision version 5, by Bruker - Product details

1

Multimodal 7T MRI Brain Imaging

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MRI studies were performed on a 7.0 T magnet (Bruker, PharmaScan, Karlsruhe, Germany), equipped with an actively shielded gradient system (14 cm inner diameter). A surface coil (2.3×1.5 cm) was used for brain imaging. Rats were anesthetized using facemask inhalation of 1.8% isoflurane by isoflurane anesthesia system (JD Medical Dist. Co. Inc., Phoenix, AZ, USA). CBF images were obtained from continuous arterial spin labeling recovery (echo-planar fluid-attenuated inversion recovery) sequences. CBF images were reconstructed with Para Vision version 5.1 software (Bruker, PharmaScan), acquisition parameters were FV = 40×40 mm, TR =18,000 ms, TE =26 ms, matrix size =128×128, and the number of excitations =1.
Multislice coronal spin-echo DWI were acquired with an echo planar diffusion-trace MRI sequence (matrix size =128×128, TR =7,100 ms, TE =22 ms, FOV =33×33 mm²). DWI images were reconstructed with Para Vision version 5.1 software (Bruker, PharmaScan).

Zhang H.M., Chen W., Liu R.N, & Zhao Y. (2018). Notch inhibitor can attenuate apparent diffusion coefficient and improve neurological function through downregulating NOX2-ROS in severe traumatic brain injury. Drug Design, Development and Therapy, 12, 3847-3854.

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2

Cerebral Perfusion Evaluation via ASL-MRI

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CBF images are ideal to evaluate the extent of cerebral perfusion after pMCAO. CBF images were obtained from continuous ASL with echo-planar imaging fluid-attenuated inversion recovery (EPI-FLAIR) sequences. CBF images were reconstructed with paravision version 5.1 software (Bruker, PharmaScan, Germany). Acquisition parameters were TR/TE = 18000/25 ms, FOV = 3.0 × 3.0 cm, matrix size = 128 × 128, and the number of excitations (NEX) = 1. CBF was measured in the ipsilateral and contralateral hemispheres. Then, the relative cerebral blood flow (rCBF) was calculated using the equation: rCBF = (ipsilateral CBF/contralateral CBF) × % [33 (link)].

Zhang J., Zou H., Zhang Q., Wang L., Lei J., Wang Y., Ouyang J., Zhang Y, & Zhao H. (2016). Effects of Xiaoshuan enteric-coated capsule on neurovascular functions assessed by quantitative multiparametric MRI in a rat model of permanent cerebral ischemia. BMC Complementary and Alternative Medicine, 16, 198.

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3

MRS Metabolite Quantification in PFC and HP

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After shimming and water suppression, ¹H spectra were acquired using a PRESS (Point RESolved Spectroscopy) sequence with 2018 sampling points, TR = 2,500 ms, TE = 20 ms, FOV = 3 × 2 × 2 (for PFC), FOV = 3 × 3 × 2 (for HP), and MTX = 256 × 256, and the resulting spectra were Fourier transformed; after the baseline correction, the spectra were measured at the corresponding chemical shifts.
Both the PFC and HP were selected as regions of interest (ROIs), as shown in Figure 2. DTI and ASL images were processed using ParaVision version 5.1 software (Bruker BioSpin Corporation, MA, USA). After the importation of MRS data into Paravision, configured TopSpin 2.0 software (Bruker BioSpin Corporation, MA, USA) was used to obtain the metabolite spectra, the baseline correction was performed to calculate the area under the curve, and the NAA/Cr (N-acetyl aspartate/creatine), Cho/Cr (choline/creatine), Glu/Cr (glutamate/creatine), and mI/Cr (myo-inositol/creatine) ratios were determined for comparisons between groups.

Zhao Z., Zhang W., Zhang Y., Zhao Y., Zheng C., Tian H., Lei J., Liu Y., Zhao R, & Tang Q. (2020). Multimodal Magnetic Resonance Imaging and Therapeutic Intervention With Yi-nao-jie-yu Decoction in a Rat Model of Post-stroke Depression. Frontiers in Psychiatry, 11, 557423.

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Preclinical MRI of Carotid Arteries

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Rats were placed prone in a cradle under the general anesthesia with an inhalation of isoflurane (1%~2.5%). The rat’s head was fixed using ear bars and a tooth bar. Body temperature was maintained between 35.3 and 37.3 °C by a flow of warm air using a heater system.
MR measurements were conducted on a 7-T preclinical scanner (BioSpec 70/20 USR, Bruker BioSpin MRI GmbH, Ettlingen, Germany) with a quadrature transmit-receive volume coil to detect MRI signals (inner diameter 72 mm, #T9562, Bruker BioSpin). MRI data were then acquired with the dedicated operation software (ParaVision (version 5.1), Bruker BioSpin). To obtain morphological information on carotid arteries, three-dimensional time-of-flight MR angiography (MRA) was performed with the following acquisition parameters; flow compensated gradient echo pulse sequence, TR 30 msec, TE 2.52 msec, flip angle 40°, field of view (FOV) 32 × 32 × 16 mm³, acquisition matrix size 160 × 160 × 80, isotropic spatial resolution 200 µm, axial orientation, number of averages = 1, and scan time approximately 6.5 minutes.

Oka M., Shimo S., Ohno N., Imai H., Abekura Y., Koseki H., Miyata H., Shimizu K., Kushamae M., Ono I., Nozaki K., Kawashima A., Kawamata T, & Aoki T. (2020). Dedifferentiation of smooth muscle cells in intracranial aneurysms and its potential contribution to the pathogenesis. Scientific Reports, 10, 8330.

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5

Cerebral Vascular MRA Analysis

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Three-dimensional time-of-flight (TOF) magnetic resonance angiography (MRA) was applied to determine the status of the circle of Willis by using a fast- low- angle shot sequence. The data set images and maximal intensity projection (MIP) of MRA were acquired by Paravision version5.1 software (Bruker, Pharmascan, Germany). The vascular signal intensities in the anterior cerebral artery (ACA), MCA, ICA, and posterior cerebral artery (PCA) were obtained (Kara et al., 2012 (link)).

Zhan Y., Li M.Z., Yang L., Feng X.F., Zhang Q.X., Zhang N., Zhao Y.Y, & Zhao H. (2019). An MRI Study of Neurovascular Restorative After Combination Treatment With Xiaoshuan Enteric-Coated Capsule and Enriched Environment in Rats After Stroke. Frontiers in Neuroscience, 13, 701.

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Cerebral Blood Flow Measurement by ASL-MRI

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CBF levels were measured by arterial spin labelling (ASL) MRI. MRI scans were conducted using a 9.4-T MRI scanner (Bruker; Bremen, Germany) with a self-shielded gradient system (12 cm in diameter) and a 23-mm surface coil. The system was connected to Topspin version 2.1 and Paravision version 5.1 software (Bruker; Bremen, Germany). The procedures for the MRI tests and the parameters of the MRI system were set according to the instructions of the machine. Briefly, mice were anaesthetized with inhaled isoflurane (4% for induction and 1.5% for maintenance). Heart rate, respiratory rate as well as body temperature were continuously monitored. T2-weighted images were obtained by using rapid acquisition with relaxation enhancement (RARE) with the following parameters: RARE factor, 8; field of view (FOV), 20 × 20 mm; repetition time (TR)/echo time (TE), 10104.89/42.0 ms; matrix size, 256 × 256; slice thickness, 0.5 mm; the number of slices, 15. ASL images were obtained from the T2-weighted images and then reconstructed using Paravision version 5.1 software. Within the ASL images, we selected 8 regions of interest (ROIs), i.e., the bilateral cortex, hippocampus, thalamus, and amygdala, for CBF measurement.

Liu S., Lei Q., Liu Y., Zhang X, & Li Z. (2022). Acoustic Stimulation Improves Memory and Reverses the Contribution of Chronic Sleep Deprivation to Pathology in 3xTgAD Mice. Brain Sciences, 12(11), 1509.

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7

In vivo and ex vivo MR imaging protocol

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In vivo MR imaging scans were performed using a horizontalbore, 7 T small-animal MR tomograph with a maximum gradient strength of 290 mT/m (ClinScan; Bruker BioSpin MR imaging). T 2weighted images (referred to as tse3DT 2 in the following sections) were used for PET image fusion and region-of-interest definitions using PMOD, version 3.2, image view and fusion tools (PMOD Technologies). Sequence details for all MR imaging sequences are detailed in the Supplemental Methods. rCBF measurements were conducted with single-slice pulsed ASL using a flow-sensitive alternating inversion recovery true fast imaging with steady-state precession approach (21) . ASL MR imaging data were analyzed using a simplified version of the Bloch equation (Supplemental Methods) and Matlab, version R2009a (The MathWorks), with an in-house-programmed routine.
Ex vivo microscopic MR imaging scans were performed at the Centre for Advanced Imaging, Brisbane, Australia, on a vertical-bore smallanimal MR scanner operating at 16.4 T (Avance II; Bruker BioSpin) using a Micro 2.5 gradient system, a 15 mm SAW volume coil, and ParaVision, version 5.1. T 2 *-weighted (referred to as highres-3DT 2 *) images at high resolution were used for MR imaging-based amyloid plaque quantification.

Maier F.C., Keller M.D., Bukala D., Bender B., Mannheim J.G., Brereton I.M., Galloway G.J, & Pichler B.J. (2015). Quantification of β-Amyloidosis and rCBF with Dedicated PET, 7 T MR Imaging, and High-Resolution Microscopic MR Imaging at 16.4 T in APP23 Mice. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 56(10).

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8

Quantifying White Matter Integrity via DTI

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Fractional anisotropy (FA) is one of the most sensitive DTI parameter for detecting the integrity of white matter fibers after cerebral damage [31 (link)]. DTI was acquired using an axial single-shot spin echo-planar sequence with a TR/TE = 6300/25 ms, 30 diffusion encoding directions, two b values = 0 and 1000 s/mm². FA images were reconstructed with paravision version 5.1 software (Bruker, Pharmascan, Germany). FA was measured in the following four regions: ipsilateral cortex and striatum, contralateral cortex and striatum. The relative FA (rFA) was calculated by comparing the parameters in the lesion ROIs (Regions of interest) with the mirrored ROIs of the contralateral side [32 (link)].

Zhang J., Zou H., Zhang Q., Wang L., Lei J., Wang Y., Ouyang J., Zhang Y, & Zhao H. (2016). Effects of Xiaoshuan enteric-coated capsule on neurovascular functions assessed by quantitative multiparametric MRI in a rat model of permanent cerebral ischemia. BMC Complementary and Alternative Medicine, 16, 198.

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9

Magnetic Resonance Angiography for Cerebral Arteries

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MRA images performed the morphological alterations of arteries. MRA images were acquired by time-of-flight (TOF) angiography with a three-dimensional (3D) Fast Low Angle Shot (FLASH) method. The scan parameters were set as follows: TR/TE = 15/2.5 ms, FOV = 3.5 × 3.5 × 4.0 cm, Matrix size = 256 × 256 × 128, and NEX = 1. MRA images were reconstructed with paravision version 5.1 software (Bruker, Pharmascan, Germany). The signal intensity of ipsilateral cerebral artery was analysed by Image J software [34 (link)].

Zhang J., Zou H., Zhang Q., Wang L., Lei J., Wang Y., Ouyang J., Zhang Y, & Zhao H. (2016). Effects of Xiaoshuan enteric-coated capsule on neurovascular functions assessed by quantitative multiparametric MRI in a rat model of permanent cerebral ischemia. BMC Complementary and Alternative Medicine, 16, 198.

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10

T2 Relaxometry Mapping for Cerebral Edema Assessment

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T2 relaxometry mapping could provide T2 values which are used to evaluate post-ischemia cerebral edema [29 (link), 30 (link)]. T2 relaxometry maps were acquired using multi-slice-multi-echo (MSME) sequences by applying 16 TEs, from 11 to 176 ms, TR = 2500 ms, FOV = 3.3 × 3.3 cm, and Matrix size = 256 × 256. In all animals, the T2 values were calculated for ipsilateral cortex and striatum based on T2 relaxometry maps that were reconstructed by paravision version 5.1 software (Bruker, Pharmascan, Germany).

Zhang J., Zou H., Zhang Q., Wang L., Lei J., Wang Y., Ouyang J., Zhang Y, & Zhao H. (2016). Effects of Xiaoshuan enteric-coated capsule on neurovascular functions assessed by quantitative multiparametric MRI in a rat model of permanent cerebral ischemia. BMC Complementary and Alternative Medicine, 16, 198.

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Paravision version 5

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13 protocols using paravision version 5

Multimodal 7T MRI Brain Imaging

Cerebral Perfusion Evaluation via ASL-MRI

MRS Metabolite Quantification in PFC and HP

Preclinical MRI of Carotid Arteries

Cerebral Vascular MRA Analysis

Cerebral Blood Flow Measurement by ASL-MRI

In vivo and ex vivo MR imaging protocol

Quantifying White Matter Integrity via DTI

Magnetic Resonance Angiography for Cerebral Arteries

T2 Relaxometry Mapping for Cerebral Edema Assessment

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