Name: real-time fmri brain mapping in animals
Uploaded: 2020-09-24T12:30:00
Description: Watch this Scientific Journal Video about Real-Time fMRI Brain Mapping in Animals at JoVE.com

We thank Dr. D. Chen and Dr. C. Yen for sharing the AFNI script to set up the real-time fMRI for PV 5 and the AFNI team for the software support. This research was supported by NIH Brain Initiative funding (RF1NS113278-01, R01 MH111438-01), and the S10 instrument grant (S10 RR023009-01) to Martinos Center, German Research Foundation (DFG) Yu215/3-1, BMBF 01GQ1702, and the internal funding from Max Planck Society.

This study was performed in accordance with the German Animal Welfare Act (TierSchG) and Animal Welfare Laboratory Animal Ordinance (TierSchVersV). The experimental protocol described here was reviewed by the ethics commission (&#167;15 TierSchG) and approved by the state authority (Regierungspr&#228;sidium, T&#252;bingen, Baden-W&#252;rttemberg, Germany).
1. Preparing the BOLD-fMRI experimental set-up for small animal study
<ol>
	<li>Turn on the console software to control imaging parameter...

<ol>
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B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+animal+functional+magnetic+resonance+imaging+and+its+application+to+neurophamacological+studies.">Real-time animal functional magnetic resonance imaging and its application to neurophamacological studies.</a> Magnetic Resonance Imaging. 26 (9), 1266-1272 (2008).</li><li>Cox, R. W., Jesmanowicz, A., Hyde, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+functional+magnetic+resonance+imaging.">Real-time functional magnetic resonance imaging.</a> Magnetic Resonance Medicine. 33 (2), 230-236 (1995).</li><li>Lee, C. C., Jack, C. R., Rossman, P. J., Riederer, S. 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W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AFNI:+Software+for+analysis+and+visualization+of+functional+magnetic+resonance+neuroimages.">AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages.</a> Computers and Biomedical Research. 29 (3), 162-173 (1996).</li><li>Liou, W. W., Goshgarian, H. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+assessment+of+the+effect+of+chronic+phrenicotomy+on+the+induction+of+the+crossed+phrenic+phenomenon.">Quantitative assessment of the effect of chronic phrenicotomy on the induction of the crossed phrenic phenomenon.</a> Experimental Neurology. 127 (1), 145-153 (1994).</li><li>Shih, Y. 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Real-time monitoring of the fMRI signal helps experimenters adjust the physiology of animals to optimize functional mapping. Motion artifacts in awake animals, as well as the anesthetic effect, are major factors that mediate the variability of fMRI signals, confounding the biological interpretation of the signal by itself31,32,33,34,35,<sup class="x...

Functional Magnetic Resonance Imaging (fMRI) is a non-invasive method to measure the hemodynamic responses1,2,3,4,5,6,7,8,9, e.g., the blood-oxygen-level-dependent (BOLD), cerebral blood volume and flow signal, associated with neural activity in the brain. In animal studies, hemodynamic signals can be affected by anesthesia10, the stress level of awake animals11, as well as the potential non-physiological artifacts, e.g., cardiac pulsation and respiratory motions12,13,14,15. Although many post-processing methods have been developed to provide a retrospective analysis of the fMRI signal for the task-related and resting-state functional dynamics and connectivity mapping16,17,18,19, there are few techniques to provide a real-time brain function mapping solution and instantaneous readouts in the animal brain20 (most of which are mainly used for human brain mapping21,22,23,24,25,26,27). In particular, this kind of real-time fMRI mapping method is lacking in animal studies. It is necessary to set up an fMRI platform to enable the investigation of real-time brain state-dependent physiological stages and to provides real-time biofeedback stimulation paradigm for animal brain functional studies.
In the present work, we illustrate a real-time fMRI experimental set-up with the customized macro-functions of the MRI console software, demonstrating real-time monitoring of the evoked BOLD-fMRI responses in the primary forepaw somatosensory cortex (FP-S1) of the anesthetized rats. This real-time set-up allows for the visualization of the ongoing brain activation in functional maps, as well as individual time courses in a voxel-wise manner, using the existing neuroimage analysis software, Analysis of Functional NeuroImages (AFNI)28. The preparation of the real-time fMRI experimental set-up for the animal study is described in the protocol. Besides the animal set-up, we provide detailed procedures to set up the visualization and analysis of the real-time fMRI signals using the latest console software in parallel with the image processing scripts. In summary, the proposed real-time fMRI set-up for animal studies is a powerful tool for monitoring the dynamic fMRI signals in the animal brain using the MRI console system.

<table>
	<tbody>
		<tr>
			<td>14.1T Bruker MRI system</td>
			<td>Bruker BioSpin MRI GmbH</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>A365 Stimulus Isolator</td>
			<td>World Precision Instruments</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>AcqKnowledge Software</td>
			<td>Biopac</td>
			<td>RRID:SCR_014279, http://www.biopac.com/product/acqknowledge-software/</td>
			<td></td>
		</tr>
		<tr>
			<td>AFNI</td>
			<td>Cox, 1996</td>
			<td>RRID:SCR_005927, http://afni.nimh.nih.gov</td>
			<td></td>
		</tr>
		<tr>
			<td>CO2SMO (ETCO2/SpO2 Monitor), Model 7100</td>
			<td>Novametrix Medical Systems Inc</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Isoflurane</td>
			<td>CP-Pharma</td>
			<td>Cat# 1214</td>
			<td></td>
		</tr>
		<tr>
			<td>Master-9</td>
			<td>A.M.P.I</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanoliter Injector</td>
			<td>World Precision Instruments</td>
			<td>Cat# NANOFIL</td>
			<td></td>
		</tr>
		<tr>
			<td>Pancuronium Bromide</td>
			<td>Inresa Arzneimittel</td>
			<td>Cat# 34409.00.00</td>
			<td></td>
		</tr>
		<tr>
			<td>ParaVision 6</td>
			<td>Bruker BioSpin MRI GmbH</td>
			<td>RRID:SCR_001964</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline (PBS)</td>
			<td>Gibco</td>
			<td>Cat# 10010-023</td>
			<td></td>
		</tr>
		<tr>
			<td>Rat: Sprague Dawley rat</td>
			<td>Charles River Laboratories</td>
			<td>Crl:CD(SD)</td>
			<td></td>
		</tr>
		<tr>
			<td>SAR-830/AP Ventilator</td>
			<td>CWE</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>&#945;-chloralose</td>
			<td>Sigma-Aldrich</td>
			<td>Cat# C0128-25G;RRID</td>
			<td></td>
		</tr>
	</tbody>
</table>

real-time fmri brain mapping in animals

Dynamic fMRI responses vary largely according to the physiological conditions of animals either under anesthesia or in awake states. We developed a real-time fMRI platform to guide experimenters to monitor fMRI responses instantaneously during acquisition, which can be used to modify the physiology of animals to achieve desired hemodynamic responses in animal brains. The real-time fMRI set-up is based on a 14.1T preclinical MRI system, enabling the real-time mapping of dynamic fMRI responses in the primary forepaw somatosensory cortex (FP-S1) of anesthetized rats. Instead of a retrospective analysis to investigate confounding sources leading to the variability of fMRI signals, the real-time fMRI platform provides a more effective scheme to identify dynamic fMRI responses using customized macro-functions and a common neuroimage analysis software in the MRI system. Also, it provides immediate troubleshooting feasibility and a real-time biofeedback stimulation paradigm for brain functional studies in animals.

Figure 3 and Figure 4 show a representative real-time voxel-wise BOLD-fMRI time course and functional maps with electrical forepaw stimulation (3 Hz, 4 s, pulse width 300 us, 2.5 mA). The fMRI design paradigm comprises 10 pre-stimulation scans, 3 stimulation scans, and 12 inter-stimulation scans with a total of 8 epochs (130 scans). The total scan time is 3 min 15 sec (195 sec). Figure 3 shows the voxel-wise time course (black line)...

Watch this Scientific Journal Video about Real-Time fMRI Brain Mapping in Animals at JoVE.com

Real-Time fMRI Brain Mapping in Animals

Animal brain functional mapping can benefit from the real-time functional magnetic resonance imaging (fMRI) experimental set-up. Using the latest software implemented in the animal MRI system, we established a real-time monitoring platform for small animal fMRI.

Dynamic fMRI responses vary largely according to the physiological conditions of animals either under anesthesia or in awake states. We developed a ...

Instead of retrospective analysis to investigate compounding sources. The proposed leader time fMRI platform provides a more effective scheme for identifying dynamic fMRI response using the latest console software. This technique can provide immediate troubleshooting feasibility and a real-time biofeedback simulation paradigm for brain functional studies in animals To acquire anatomical images covering the whole brain in the coronal view, click the continue button to run a T2 weighted rare sequence.To set up the realtime fMRI software. Open a terminal window and use the command to navigate to the realtime AFNI plugin path. Use the commands as indicated to execute the AFNI software with the realtime plugin.Use the diamond command and options to monitor the upcoming AFNI brick files. Use the PVC MD command with the options as indicated, to run the background macro script. To obtain the EPI acquisition parameters, use the exec PVC MD command and options.To convert the 3D ECHO planar imaging raw data, to AFNI files, in real time, in the background macro script. Use the exec TOD-3D Command and options, making sure that EPI geometrical information is consistent with the anatomy orientation. Click the continue button to run a T2 Star Weighted 3D EPI Sequence for bold fMRI imaging.To overlay the EPI images, onto the anatomical rare images. First, use the command to convert the rare images to an AFNI Brick dataset and use the script and options to register the EPI images to the anatomical images. To process resting-state functional connectivity maps of the bold responses.Use AFNI options to calculate the seed based correlation of the 3D plus time dataset, such as resting state fMRI time series. Then to visualize functional maps of the bold signals, select the defined overlay option and use the clusters function, from the AFNI user interface menu, to generate an interactive clustering in the AFNI software. To visualize response electrical stimulation responses by fMRI.Turn on an electrical stimulus isolator and use stimulation blocks to perform electrical four-paw stimulation for one evoked fMRI analysis. In this Representative Real-Time Voxel-Wise Bold fMRI Time Course. The voxel-wise time course of the contralaterally primary four-paw somatosensory cortex, corresponding to the block design paradigm in the real-time acquisition format, after electrical four-paw stimulation can be observed.As illustrated activated bold maps corresponding to the electrical four-paw stimulation can also be generated with the activated regions detected and displayed as colored clusters. Be sure to activate the 3D EPI Reconstruction option pre-image 3D activity and execute macro in the data construction user interface menu. And to link to the predefining macro script set-up RT 3D API before scanning.

Research

JoVE Journal

Neuroscience

Simultaneous fMRI and Electrophysiology in the Rodent Brain

To examine the neural basis of the blood oxygenation level dependent (BOLD) magnetic resonance imaging (MRI) signal, we have developed a rodent model in ...

Combining Transcranial Magnetic Stimulation and fMRI to Examine the Default Mode Network

The default mode network is a group of brain regions that are active when an individual is not focused on the outside world and the brain is at "wakeful ...

Recording Human Electrocorticographic (ECoG) Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

Recording Human Electrocorticographic ECoG Signals for Neuroscientific Research and Real-time Functional Cortical Mapping

Neuroimaging studies of human cognitive, sensory, and motor processes are usually based on noninvasive techniques such as electroencephalography (EEG), ...

Design and Assembly of an Ultra-light Motorized Microdrive for Chronic Neural Recordings in Small Animals

The ability to chronically record from populations of neurons in freely behaving animals has proven an invaluable tool for dissecting the function of ...

Functional Imaging of Auditory Cortex in Adult Cats using High-field fMRI

Current knowledge of sensory processing in the mammalian auditory system is mainly derived from electrophysiological studies in a variety of animal ...

Deep Brain Stimulation with Simultaneous fMRI in Rodents

In order to visualize the global and downstream neuronal responses to deep brain stimulation (DBS) at various targets, we have developed a protocol for ...

Rapid Genotyping of Animals Followed by Establishing Primary Cultures of Brain Neurons

High-resolution analysis of the morphology and function of mammalian neurons often requires the genotyping of individual animals followed by the analysis ...

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

An Ex Vivo Laser-induced Spinal Cord Injury Model to Assess Mechanisms of Axonal Degeneration in Real-time

Injured CNS axons fail to regenerate and often retract away from the injury site. Axons spared from the initial injury may later undergo secondary axonal ...

A Protocol for the Administration of Real-Time fMRI Neurofeedback Training

Neurologic disorders are characterized by abnormal cellular-, molecular-, and circuit-level functions in the brain. New methods to induce and control ...

Real-time Iontophoresis with Tetramethylammonium to Quantify Volume Fraction and Tortuosity of Brain Extracellular Space

This review describes the basic concepts and protocol to perform the real-time iontophoresis (RTI) method, the gold-standard to explore and quantify the ...