Idiosyncrasies of acquiring data from small animals#

Rationale#

Many parts of the acquisition procedure differ between human and small animal scanning. Moreover, while human scans are almost always driven by a specialist radiographer, small animal scans are often controlled by researchers themselves. The “Do-It-Yourself” experience provides preclinical researchers a grassroots understanding of data quality that researchers working with humans may find difficult to obtain.

Hardware#

Magnet field strength#

The scanner’s field strength, which typically ranges from 4.7 to 16.4 Tesla for preclinical imaging, can itself have many impacts on the data quality: higher field strength provides higher signal-to-noise ratios, but it also exacerbates many types of artifacts.

Scanner manufacture#

Bruker currently has a monopoly in preclinical imaging, but many sites have older scanners from other manufacturers. Those with Bruker scanners may also have a maintenance package which includes tests for quality assurance.

Coils#

Some volume coils require manual tuning. For scanners from out-of-business manufacturers, “homemade” coils are more common. These coils use known standards in day-to-day scanning, so are possibly more standardised in terms of replicability, but may be less standardised across sites. Cryocoils are increasingly available but not yet ubiquitous.

Physiological monitoring#

While the requirements for accurate physiological monitoring is explained in more detail below, there are many pieces of hardware that can be discussed. This minimally includes rectal thermometers and respiration balloons, but can also include pulse oximeters and/or invasive blood pressure monitoring.

Other hardware#

Cradles, bite bars, ear bars, pillows can be provided by the scanner manufacturer or “homemade”. These facilitate support of the animal in the scanner and reduce movement.

Software#

Scanner software#

Related to scanner manufacture, is the software used to acquire and reconstruct the images. Bruker’s software, Paravision, has several versions available. Paravision generates 2dseq files and can export DICOM images commonly generated by human scanners. However, storage of metadata may not always be consistent with human imaging standards.

Other software#

Similarly, various software is available for monitoring physiology which is discussed at length below. As the animals are often anaesthetised, task-based fMRI is less common. Instead, experiments may generate evoked-responses to some stimulus (e.g. stimulating a paw with electricity) in the scanner. Thus, software is also required to synchronise the stimulus onset to the scanning acquisition. Such software can also be used for the inverse task: by gating acquisitions the scanner will only acquire data at certain times (e.g., during a certain section of the respiratory cycle).

Anatomy#

Scale#

An obvious difference between small animals and humans is the scale of their brains. Adult human brain volumes are approximately 1200 cm3, while adult rat brains are approximately 2.5 cm3 and mice brain volumes are smaller still. This difference in scale necessitates the increased magnet field strength but the change in field strength is not proportional to the change in size.

Tissue differences#

The proportion of white matter in rodents is smaller than that in humans. Since white matter bundles are much less distinct in rats and mice, the MR signal contrast between the two tissue types is often less well-defined.

Additionally, the olfactory bulb is much larger in rodents than in humans and there is no cortical folding.

Orientation#

As bipeds, the human brain sits on top of the spinal cord and consequently the rostrocaudal plane is curved along the anterioposterior and superoinferior planes. In quadripeds, like rodents, the anterioposterior and rostrocaudal planes are equivalent.

Additionally, I have noticed confusion in the convention for naming the scanner orientations. Humans most often enter the scanner supine along the axis that aligns with that of B0, i.e., the B0 field axis aligns with the superior-inferior axis. Rodents are likely to be prone (although not always) and because of the difference in anatomical orientation described above, the posterior-anterior plane in quadripeds aligns with the B0 field axis.

Thus orientation may be “scanner-oriented” (where the axes aligns with the magnetic field directions) or “subject-oriented” (where the axes align with the anatomy of the subject).

Strain#

There may be differences in anatomy or physiology that come from differences in species strain. In particular, genetically modified animals may be more susceptible to larger ventricular compartments. Another example may be an increase in bodyweight which can have downstream effects on anaesthesia.

Physiology#

Anaesthesia and sedation#

It is common for animals to be anaesthetised or sedated for MRI to reduce motion. Different anaesthetics and sedatives act through different pathways, and each come with benefits and costs.

Compound

Administration

Benefits

Costs

Isoflurane

inhalation

  • non-invasive administration
  • Short recovery

    		•

  • Uncouples BOLD response
  • Dangerous cumulative effects

    		•

    (Dex)meditomidine

    infusion

  • preserves BOLD response

  • requires Atipamezole for speedy recovery

    		•

    Alpha-Chloralose

    infusion

  • preserves BOLD response

  • requires cannulation
  • Difficult recovery

    		•

    Ketamine

    infusion

  • established anaesthetic
  • single administration has long effects
  • easily reversible

    		•

  • confound with BOLD response

    		•

    Halothane

    inhalation

  • non-invasive administration
  • preserves BOLD response

    		•

  • toxic
  • increasingly hard to acquire

    		•

    Respiration#

    Respiration rate and the pattern of inhalation is impacted by the choice of anaesthesia or sedative. Often anaesthetic procedures prescribe a respiration rate to standardise across animals, with a wider range of rates for anaesthetic delivery.

    Thermal homeostasis#

    Small animals, particularly mice, find it difficult to regulate their body temperature in the scanner, especially when unconscious. Consequently, internal body temperature is recorded with a thermometer. It is possible to use the thermometer reading as part of a feedback loop controlling either a water heating system (built in to the bed or applied as a heated blanket) or an air heating system (which is blown through the scanner bore with a fan) with all the possible problems related to frequency shifts and drifting that could affect the scans.

    Since temperature is critical for the rate of oxygen consumption, temperature should be maintained within a small normative range.

    Movement#

    Movement is often reduced in animal imaging due to the use of bite bars, ear bars, and anaesthesitics and sedatives. However, movement should still be carefully scrutinized as it may point to:

    • less anaesthetised/sedated state

    • movement associated with the onset of a task (e.g. jumping at stimulus)

    • scanner drift

    Hands-on#

    Let’s see some of these factors in action. The acquisition notebook has examples of data that have poor acquisition. Can you guess where they have deviated from the standard operating procedure?