Acquisition of Resting-State Functional Magnetic Resonance Imaging Data in the Rat

Summary

This protocol describes a method for obtaining stable resting-state functional magnetic resonance imaging (rs-fMRI) data from a rat using low dose isoflurane in combination with low dose dexmedetomidine.

Abstract

Resting-state functional magnetic resonance imaging (rs-fMRI) has become an increasingly popular method to study brain function in a resting, non-task state. This protocol describes a preclinical survival method for obtaining rs-fMRI data. Combining low dose isoflurane with continuous infusion of the α₂ adrenergic receptor agonist dexmedetomidine provides a robust option for stable, high-quality data acquisition while preserving brain network function. Furthermore, this procedure allows for spontaneous breathing and near-normal physiology in the rat. Additional imaging sequences can be combined with resting-state acquisition creating experimental protocols with anesthetic stability of up to 5 h using this method. This protocol describes the setup of equipment, monitoring of rat physiology during four distinct phases of anesthesia, acquisition of resting-state scans, quality assessment of data, recovery of the animal, and a brief discussion of post-processing data analysis. This protocol can be used across a wide variety of preclinical rodent models to help reveal the resulting brain network changes that occur at rest.

Introduction

Resting-state functional magnetic resonance imaging (rs-fMRI) is a measure of the blood-oxygen-level-dependent (BOLD) signal when the brain is at rest and not engaged in any particular task. These signals can be used to measure correlations between brain regions to determine the functional connectivity within neural networks. rs-fMRI is widely used in clinical studies due to its non-invasiveness and the low amount of effort required of patients (as compared to task-based fMRI) making it optimal for diverse patient populations¹.

Technological advances have allowed rs-fMRI to be adapted for use in rodent models to unco....

Protocol

All experiments were performed on a 9.4 T MRI scanner, and were approved by the Institutional Animal Care and Use Committee at Dartmouth College. Additional approval was obtained to record and show the animals used in the video and figures below.

1. Preparations before scanning

1. Subcutaneous infusion line
   1. Partially remove a 23 G needle from its package so that the needle point remains sterile.
   2. Securely hold the hub of the needle and use a razor blade to score .......

Discussion

Stability of the animal, both physically and physiologically, is key to obtaining high-quality resting-state data. This protocol achieves stability by moving through four distinct phases of anesthesia. It is imperative that the animal has met the set physiological thresholds before moving to the next phase of anesthesia; since this method relies on physiological autoregulatory mechanisms, individual animals may require slightly different amounts of time at each anesthesia phase. It is our experience that taking more time.......

Materials

Name	Company	Catalog Number	Comments
9.4T MRI	Varian/Bruker		Varian upgraded with Bruker console running Paravision 6.0.1 software
Air-Oxygen Mixer	Sechrist	Model 3500CP-G
Analysis of Functional NeuroImages (AFNI)	NIMH/NIH	Version AFNI_18.3.03	Freely available at: https://afni.nimh.nih.gov/
Animal Cradle	RAPID Biomedical	LHRXGS-00563	rat holder with bite bar, nose cone and ear bars
Animal Physiology Monitoring & Gating System	SAII	Model 1025	MR-compatible system including oxygen saturation, temperature, respiration and fiber optic pulse oximetry add-on
Antisedan (atipamezole hydrochloride)	Patterson Veterinary	07-867-7097	Zoetis, Manufacturer Item #10000449
Ceramic MRI-Safe Scissors	MRIequip.com	MT-6003
Clippers	Patterson Veterinary	07-882-1032	Wahl touch-up trimmer combo kit, Manufacturer Item #09990-1201
Dexmedesed (dexmedetomidine hydrochloride)	Patterson Veterinary	07-893-1801	Dechra Veterinary Products, Manufacturer Item#17033-005-10
Digital Rectal Thermometer Covers	Medline	MDS9608
FMRIB Software Library	FMRIB	MELODIC Version 3.15	Freely available at: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
Heating Pad	Cara Inc.	Model 50
Hemostat forceps, straight	Kent Scientific	INS750451-2
Isoflurane	Patterson Veterinary	07-893-1389	Patterson Private Label, Manufacturer Item #14043-0704-06
Isoflurane Vaporizer	VetEquip Inc.	911103
Lab Tape, 3/4"	VWR International	89097-990
Needles, 23 gauge	BD	305145	plastic hub removed
Parafilm Laboratory Film	Patterson Veterinary	07-893-0260	Medline Industries Inc., Manufacturer Item #HSFHS234526A
Planar Surface Coil	Bruker	T12609	2cm
Polyethylene Tubing	Braintree Scientific	PE50 50FT	0.023" (inner diameter), 0.038" (outer diameter)
Puralube Ophthalmic Ointment	Patterson Veterinary	07-888-2572	Dechra Veterinary Products, Manufacturer Item #211-38
Sprague Dawley Rats	Charles River	400 SAS SD
Sterile 0.9% Saline Solution	Patterson Veterinary	07-892-4348	Aspen Vet, Manufacturer Item #14208186
Sterile Alcohol Prep Pads	Medline	MDS090735
Surgical Tape, 1" (3M Durapore)	Medline	MMM15381Z	3M Healthcare, "wide medical tape"
Surgical White Paper Tape, 1/2" (3M Micropore)	Medline	MMM15300	3M Healthcare
Syringes, 1 mL w/ 25 gauge needle	BD	309626
Syringes, 3 mL	BD	309657
Vented induction and scavenging system	VetEquip Inc.	942102	2 liter induction chamber with active scavenging
		411724	omega flowmeter
		931600	scavenging cube, "vacuum"
		921616	nose cone, non-rebreathing