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Representative Results






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

Published: August 28th, 2021



1Dartmouth-Hitchcock Medical Center, 2Geisel School of Medicine at Dartmouth, 3National Institute on Drug Abuse, National Institutes of Health, 4University of Guelph
* These authors contributed equally

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.

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.

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....

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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 .......

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Following each resting-state scan, stability is assessed using an independent component analysis (ICA; example script included in Supplementary Files). Figure 6 shows examples of component outputs from resting-state scans. Figure 6a shows a signal component from a scan with high stability. Note that spatially, the component has high regionality. Within the time course below the spatial component, the signal is stable and not predictable, indicat.......

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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.......

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This work was supported by funding from the National Institute of Health (NIH)'s National Institute on Drug Abuse (NIDA) [DJW, EDKS, and EMB were supported by Grant R21DA044501 awarded to Alan I. Green and DJW was supported by Grant T32DA037202 to Alan J. Budney] and the National Institute on Alcohol Abuse and Alcoholism (NIAAA) [Grant F31AA028413 to Emily D. K. Sullivan]. Additional support was provided through Alan I. Green's endowed fund as the Raymond Sobel Professor of Psychiatry at Dartmouth.

Hanbing Lu is supported by the National Institute on Drug Abuse Intramural Research Program, NIH.

The author....

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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:
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 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:
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

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