diff --git a/docs/animal-qc/acquisition.md b/docs/animal-qc/acquisition.md index 8f21272..95bc18b 100644 --- a/docs/animal-qc/acquisition.md +++ b/docs/animal-qc/acquisition.md @@ -11,16 +11,16 @@ difficult to obtain. ## Hardware ### Magnet field strength -The scanner's field strength, which range from 4.7 to 16.4 Tesla, can itself +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 in shorter acquisition times, but it also +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 -Volume coils require manual tuning (at least) daily. +Some volume coils require manual tuning. For scanners from out-of-business manufacturers, "homemade" coils are more common and less standardised. Cryocoils are increasingly available but not yet ubiquitous. @@ -28,7 +28,7 @@ Cryocoils are increasingly available but not yet ubiquitous. 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. +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". @@ -39,14 +39,13 @@ These facilitate support of the animal in the scanner and reduce movement. 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 rather than the `DICOM` images commonly +Paravision generates `2dseq` files and can export `DICOM` images commonly generated by human scanners. -Consequently, conversion to standardised naming formats requires specialised -software that can work with these proprietary files. +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](#physiology). -As the animals are often anaesthetised task-based fMRI is less common. +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 @@ -64,7 +63,7 @@ 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 +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 @@ -78,8 +77,7 @@ 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 so the B1 field aligns with the anterior-posterior plane, and the -B0 field axis aligns with the superior-inferior axis. +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. @@ -88,7 +86,7 @@ Thus orientation may be "scanner-oriented" (where the axes aligns with the magne 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 +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. @@ -104,8 +102,8 @@ 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 cannulation
  • requires Atipamezole for speedy recovery
    • -Alpha-Chloralose | infusion |
  • preserves BOLD response
    • |
  • Difficult recovery
    • +(Dex)meditomidine | infusion |
  • preserves BOLD response
    • |
  • requires Atipamezole for speedy recovery
    • +Alpha-Chloralose | infusion |
  • preserves BOLD response
    • |
  • requires cannulation
  • Difficult recovery
    • Ketamine | infusion | | ### Respiration @@ -121,16 +119,16 @@ 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 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 scanning animal imaging due to the use of bite bars, +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 +- scanner drift ## Hands-on Let's see some of these factors in action.