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All procedures involving animal models have been reviewed by the local institutional animal care committee and the JoVE veterinary review board.&#160;1. Animal Preparation and Monitoring<ol><li>Leave all magnetically susceptible objects such as wallets, keys, credit cards,&#160;etc. outside the scanner room prior to commencing animal preparation for MRI scanning.</li><li>Initially anesthetize the rat (2-month-old male Sprague-Dawley (SD) rat, 280&#8211;350 g) in an induction box using a mixture of 5% isoflurane (ISO) and oxygen (2 L/min) for 3&#8211;5 min, as necessary.</li><li>When the animal is recumbent and exhibits no response to a tail or toe pinch, discontinue ISO administration and transfer the animal to the scanning room.</li><li>Place the rat in the MRI bed in a head-first prone position and deliver 2-3% ISO through a nose cone device for maintaining anesthesia.</li><li>Monitor respiration by placing a respiratory pillow sensor under the animal's torso.</li><li>Connect the sensor to a respiratory system and check for respiration rate between 40-50 beats per minute (bpm).</li><li>For cine-gated PC-MRI acquisition, place one electrode each on the right forepaw and the left hind paw, respectively (Figure 1a).</li><li>Twist the electrocardiography (ECG) cables together.</li><li>Use a head holder with ear bars and a bite bar to secure the animal to restrict head movement.</li><li>Use a warm air heating system or gauze pads to maintain body temperature while in the magnet.</li><li>Ensure that the R-wave is clear on the ECG monitor (Figure 1b) and place the animal in the scanner. There is no need to place the surface coil on the top of the animal's neck as images are acquired by the volume coil.</li></ol>2. MRI Acquisition<ol><li>Use 2&#8211;3% ISO to maintain anesthesia during the entire imaging procedure. Continuously monitor physiological responses and keep as constant as possible.</li><li>Start the MRI scans once the animal is placed inside the scanner and continues to be physiologically stable. In this study, use a 7 T small animal MRI system with a gradient strength of 630 mT/m, but other field strengths of small animal MRI systems can be used.</li><li>Select the&#160;"Localizer" sequence from the console monitor of the MRI scanner and acquire scout images along all three orientations using any fast image acquisition sequence,&#160;e.g., the fast spin echo, to create coronal, axial, and sagittal images. The purpose of these scout images is to determine the imaging planes.</li><li>Ensure that the center of the animal's head and neck are at the center of the magnet. If necessary, adjust the animal's position until the correct position is reached. If the animal is repositioned, repeat scanning to obtain scout images.</li><li>Select the&#160;"Time-of-flight (TOF) angiogram"&#160;sequence from the console monitor of the MRI scanner and acquire a 2D TOF angiogram first to ascertain the precise anatomical location of the common carotid artery (CCA). Use the following scanning parameters: repetition time (TR)/ echo time (TE)=22/4.87 ms, flip angle = 90&#176;, field of view (FOV) = 40 &#215; 40 mm2, matrix size = 256 &#215; 256, slice thickness 0.6 mm, with the number of excitation (NEX) = 1. NOTE: The name of the TOF sequence could be vender specific. The user can insert these parameters in the console monitor.</li><li>Ensure that the saturation band is "on" and is placed on the top to avoid interference from venous signals. NOTE:&#160;For the saturation band, it usually comes with the TOF sequence. If the saturation band does not show on the monitor, please notify the service person.</li><li>After locating the CCA using the TOF angiogram, target the image plane of the PC-MRI to the center of the CCA and orient such that the slice is perpendicular to the direction of blood flow (Figure 2a).</li><li>Ensure that both respiration and ECG gating are connected to the MRI system, showing the clear signal on the monitor computer (Figure 1b), and set the trigger module to be "on" in the&#160;"Trigger Mode" from the console monitor of the MRI scanner.</li><li>Confirm that the animal's physiological responses are stable before initiating the PC-MRI scan from the monitoring computer (Figure 1b). Verify that gating selections are "on" in both the monitor computer and the console monitor of MRI scanner. NOTE: The physiology monitoring system used in this study is provided by the vender. For most animal scanners, similar physiology monitoring systems are provided and are vender specific.</li><li>Select the sequence of PC-MRI sequence from the console monitor of the MRI scanner and perform gated PC-MRI scans using the following parameters: TR/TE=15.55/4.51 ms (minimum TR and TE), flip angle=30&#176;, FOV = 40 &#215; 40 mm2, matrix size = 192 &#215; 192, slice thickness = 2 mm, velocity encoding (VENC) = 120 cm/s, with NEX=8. Unidirectional VENC is acquired in the through-plane direction. NOTE: The scan time is approximately 8.5 min, but the actual scan time may be slightly different among animals due to the variation in cardiac cycles.</li><li>Repeat steps 2.6&#8211;2.9 of image acquisition if the region of interest (ROI) is to be changed to another location in the CCA, such as at the bifurcation.</li><li>Remove the animal from the scanner and return it to its recovery cage when the scan is complete.</li><li>Warm the animal with a heating lamp to maintain body temperature. Keep the lamp at least 15 cm away from the animal to prevent overheating.</li><li>When the animal starts to move and exhibits a response to a tail or toe pinch, turn off the heating lamp.</li></ol>

<figure class='table' style='width:581pt;'><table class='ck-table-resized'><colgroup><col style='width:30.81%;'><col style='width:20.65%;'><col style='width:20.14%;'><col style='width:28.4%;'></colgroup><tbody><tr><td style='height:15.5pt;'>7T small animal MRI system</td><td>Bruker</td><td>&#160;</td><td>&#160;</td></tr><tr><td style='height:15.5pt;'>Isoflurane</td><td>Baxter</td><td>1001936040</td><td>Anesthetic</td></tr><tr><td style='height:15.5pt;'>ECG lead</td><td>3M</td><td>2269T</td><td>&#160;</td></tr><tr><td style='height:15.5pt;'>Monitoring and gating system</td><td>SA instruments, Inc</td><td>Model 1030</td><td>&#160;</td></tr></tbody></table></figure>

 phase contrast magnetic resonance imaging to assess blood flow in the arteries of a rat

<a href='https://app.jove.com/v/57304/phase-contrast-magnetic-resonance-imaging-rat-common-carotid'>Source: Chiu, S., et al. Phase Contrast Magnetic Resonance Imaging in the Rat Common Carotid Artery. J. Vis. Exp. (2018).</a>This video demonstrates phase contrast magnetic resonance imaging (PC-MRI) to measure blood flow in the common carotid artery of a rat. After securing an anesthetized rat on the MRI bed and ensuring stable physiological parameters, the common carotid artery is scanned to capture images at defined intervals. Blood flow is then computed from these images to evaluate changes throughout the cardiac cycle.

<img src='https://cloudfront.jove.com/files/ftp_upload/23411/23411_Figure_1_editor_23411.jpg' alt='23411_Figure_1.jpg' />Figure 1: Animal monitoring. (a) ECG electrodes are placed on the right forepaw and the left hind paw, and the respiratory pillow sensor is placed under the animal's torso. (b) The ECG and respiratory signals are clearly visible on the monitor.<img src='https://cloudfront.jove.com/files/ftp_upload/23411/23411_Figur...

 Phase Contrast Magnetic Resonance Imaging to Assess Blood Flow in the Arteries of a Rat

Source: Chiu, S., et al. Phase Contrast Magnetic Resonance Imaging in the Rat Common Carotid Artery. J. Vis. Exp. (2018).This video demonstrates phase ...

Take an anesthetized rat secured on the bed of a magnetic resonance imaging, or MRI, system.Gauze pads on the rat maintain its body temperature while sensors on the body monitor respiration and cardiac activity, ensuring stable physiological parameters.Position the rat inside the scanner. Using phase contrast MRI, scan the neck region to identify the common carotid artery or CCA.The scanner detects fluctuations in MR signal intensity caused by moving protons in the blood.During the phases of the cardiac cycle, the blood velocity changes along with the diameter of the artery due to periodic constriction and dilation.Align the imaging plane perpendicular to the direction of blood flow to obtain a cross-sectional view of the arteries.Obtain images at defined intervals to compute blood flow, a product of blood velocity and the cross-sectional area, and assess variations in blood flow throughout the cardiac cycle.

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JoVE Encyclopedia of Experiments

Neuroscience

Neuroimaging

Neurovascular & Blood Flow Imaging

40 Views. Source: Chiu, S., et al. Phase Contrast Magnetic Resonance Imaging in the Rat Common Carotid Artery. J. Vis. Exp. (2018). This video demonstrates phase contrast magnetic resonance imaging (PC-MRI) to measure blood flow in the common carotid artery of a rat. After securing an anesthetized rat on the MRI bed and ensuring stable physiological parameters, the common carotid artery is scanned to capture images at defined intervals. Blood flow is then computed from these images to evaluate changes thr...

Video:  Phase Contrast Magnetic Resonance Imaging to Assess Blood Flow in the Arteries of a Rat - Concept

Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images

Within neuroimaging research, a number of recent studies have discussed the impact of between-study differences in volumetric findings that are thought to result from the use of different segmentation tools to generate brain volumes. Here, processing pipelines for seven automated tools that can be used to segment grey matter within the brain are presented. The protocol provides an initial step for researchers aiming to find the most accurate method for generating grey matter volumes from T1-weighted MRI scans. Steps to undertake detailed visual quality control are also included in the manuscript. This protocol covers a range of potential segmentation tools and encourages users to compare the performance of these tools within a subset of their data before selecting one to apply to a full cohort. Furthermore, the protocol may be further generalized to the segmentation of other brain regions.

This protocol describes the process of applying seven different automated segmentation tools to structural T1-weighted MRI scans to delineate grey matter regions that can be used for the quantification of grey matter volume.

Within neuroimaging research, a number of recent studies have discussed the impact of between-study differences in volumetric findings that are thought to ...

JoVE Journal

Functional MRI in Conjunction with a Novel MRI-compatible Hand-induced Robotic Device to Evaluate Rehabilitation of Individuals Recovering from Hand Grip Deficits

Functional magnetic resonance imaging (fMRI) is a non-invasive magnetic resonance imaging technique that images brain activation in vivo, using endogenous deoxyhemoglobin as an endogenous contrast agent to detect changes in blood-level-dependent oxygenation (BOLD effect). We combined fMRI with a novel robotic device (MR-compatible hand-induced robotic device [MR_CHIROD]) so that a person in the scanner can execute a controlled motor task, hand-squeezing, which is a very important hand movement to study in neurological motor disease. We employed parallel imaging (generalized auto-calibrating partially parallel acquisitions [GRAPPA]), which allowed higher spatial resolution resulting in increased sensitivity to BOLD. The combination of fMRI with the hand-induced robotic device allowed precise control and monitoring of the task that was executed while a participant was in the scanner; this may prove to be of utility in rehabilitation of hand motor function in patients recovering from neurological deficits (e.g., stroke). Here we outline the protocol for using the current prototype of the MR_CHIROD during an fMRI scan.

We performed functional MRI using a novel MRI-compatible hand-induced robotic device to evaluate its utility for monitoring hand motor function in individuals recovering from neurological deficits.

Functional magnetic resonance imaging (fMRI) is a non-invasive magnetic resonance imaging technique that images brain activation in vivo, using endogenous ...

Concurrent EEG and Functional MRI Recording and Integration Analysis for Dynamic Cortical Activity Imaging

Electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) are two of the fundamental noninvasive methods for identifying brain activity. Multimodal methods have sought to combine the high temporal resolution of EEG with the spatial precision of fMRI, but the complexity of this approach is currently in need of improvement. The protocol presented here describes the recently developed spatiotemporal fMRI-constrained EEG source imaging method, which seeks to rectify source biases and improve EEG-fMRI source localization through the dynamic recruitment of fMRI sub-regions. The process begins with the collection of multimodal data from concurrent EEG and fMRI scans, the generation of 3D cortical models, and independent EEG and fMRI processing. The processed fMRI activation maps are then split into multiple priors, according to their location and surrounding area. These are taken as priors in a two-level hierarchical Bayesian algorithm for EEG source localization. For each window of interest (defined by the operator), specific segments of the fMRI activation map will be identified as active to optimize a parameter known as model evidence. These will be used as soft constraints on the identified cortical activity, increasing the specificity of the multimodal imaging method by reducing cross-talk and avoiding erroneous activity in other conditionally active fMRI regions. The method generates cortical maps of activity and time-courses, which may be taken as final results, or used as a basis for further analyses (analyses of correlation, causation, etc.) While the method is somewhat limited by its modalities (it will not find EEG-invisible sources), it is broadly compatible with most major processing software, and is suitable for most neuroimaging studies.

An EEG-fMRI multimodal imaging method, known as the spatiotemporal fMRI-constrained EEG source imaging method, is described here. The presented method employs conditionally-active fMRI sub-maps, or priors, to guide EEG source localization in a manner that improves spatial specificity and limits erroneous results.

Phase Contrast Magnetic Resonance Imaging to Assess Blood Flow in the Arteries of a Rat

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Phase Contrast Magnetic Resonance Imaging to Assess Blood Flow in the Arteries of a Rat

Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images

Functional MRI in Conjunction with a Novel MRI-compatible Hand-induced Robotic Device to Evaluate Rehabilitation of Individuals Recovering from Hand Grip Deficits

Concurrent EEG and Functional MRI Recording and Integration Analysis for Dynamic Cortical Activity Imaging