In this education series we will cover the basic and advanced techniques used to perform MRI on fish brains using preclinical systems. Details will be given on 1) different fixations and their effects on relaxation measures and eventual images; 2) the use of contrast agents, including a comparison between two gadolinium based contrast agents magnevist and optimark; and 3) in situ versus ex-vivo imaging techniques.

Each permutation in methodology produces a different contrast and has implications on available coil sizes and therefore must be carefully considered prior to beginning a new study. Finally, details will also be given on brain removal for high resolution neuro-imaging of fish.

An overview of field strengths for imaging of whole brain and whole fish will be given along with details on coil selection and production of specialised holders to improve image quality via 3D printing. The presentation will focus on pulse sequences for use with 16.4T vertical bore imaging.

Details will be provided for: 1) pulse sequences for MRI, and DWI. 2) Tradeoffs on Number of averages vs scan time. 3) DWI - Tradeoffs on resolution vs number of directions, vs scan time. 4) Issues with sample movement during 5) surface vs solenoid coils.

Example images and results will be shown for barramundi whole brain with a 30mm coil, 5mm ex-vivo imaging with a brain holder at 16.4T in zebrafish, shark MRI in a search for magnetite and live imaging of zebrafish. Examples of fish brain MRI are in Figures 1 and 2Ex-vivo imaging often exhibits low contrast or artifacts such as air-bubbles, model averaging is a technique to reduce these effects. We will present details of a technique that allows you to develop phenotype based atlases using minimum deformation averaging. The session will also cover details of preparation consistency, standardised orientation and ontology issues.