Researcher’s Guide

This section attempts to give a brief “researcher’s guide” to running experimental studies at the 7T facility, from initial concept to final completion.

Contact Piotr Kozlowski (Facility Director) or Andrew Yung (Research Scientist) to discuss your research ideas.  Initial consultations will focus on the feasibility of the study.  Determined on a case-by-case basis, it may be possible to run some initial feasibility tests on the scanner prior to official study approval by the Centre.

With the help of Centre staff, the investigator will be asked to fill out and submit a MRI Protocol Proposal form (click here to download).  This document summarizes the research goals of the project, the experiment plan, sample sizes, number of scans requested, and a description of the MRI techniques.  Once submitted, the protocol proposal will be reviewed by the Centre’s 7T Protocol Committee and be sent back with questions, comments and requested amendments.   7T MRI Proposal Form Feb 15

An important part of the proposal process is the accurate estimation of the amount and type of “billable hours” that are requested, since this reflects the impact on the resources of both the investigator and the Centre.  Billable “scanning time” is considered as any duration where the facility is being used so that another MRI experiment cannot be performed (e.g. from the time an animal is anesthetized to the time it is removed from the scanner).  For the current fee schedule and cancellation policy, please click here.

Here is an overview of the different types of fees charged by the facility:

  • Development time:  awarded for developing MR protocols and experimental apparatus (including RF coils) which expand the capabilities of the facility that would benefit other researchers.  The amount of development time required for your project will be estimated by Centre staff, and may increase as the study progresses should it become necessary.  These hours are offered free of charge.  However, once the development time exceeds the allotment or becomes study specific, the hours will be considered pilot time and standard scanning time and therefore billable.
  • Pilot scanning time:  awarded at a reduced rate when scanner time is required to test the feasibility of existing MR techniques to carry out a funded research project.  Pilot time may also be rewarded for short studies that are required to generate results for use in a funding application.  The amount of pilot time used will depend on the specific experiment; however a 16-hour cap on pilot time will be imposed after which time subsequent scans will be charged at the standard scanning rate.
  • Standard scanning time:  awarded for most academic grant-funded research.
  • Industry scanning time:  awarded for industry-sponsored research.
  • Analysis time:  investigators may decide to ask the Centre staff to perform data analysis for their experiments, especially if the analysis is beyond his/her scope or expertise.  These hours will be billed separately.

The distribution of these billable hours will be determined through consultation between the investigator and Centre staff.

All researchers must have their experimental protocols approved by the Institutional Animal Care Committee (ACC) prior to starting any procedures in the Facility (go to the ACC website to find out more).  Existing ACC protocols may be amended to reflect the MRI experiment. We can provide details regarding the MRI techniques and animal care issues specifically related to the use of the facility that are required to complete the ACC protocol. The Centre also has an approved ACC protocol for scanning of control animals which may be appropriate for initial test studies.

The 7T Facility does not provide overnight boarding facilities for animals - researchers are responsible for arranging their own animal housing. We suggest that researchers with survival experiments take advantage of the animal holding facilities provided in the Animal Resource Unit. This is a conventional animal facility that has rooms that are designated for housing rats and mice specifically for researchers, as well as surgical rooms available for use. There is an option of ordering animals directly through them. The Centre can also order animals for its researchers and bill them later.

Researchers are required to provide the most recent animal health record from their animal housing facility before initiating a MRI study, and are responsible for providing updated health records as they become available. As a general rule of thumb, the health record should be at most 6 months old (more recent is preferred) at the time of the MRI experiment.  MRI studies may be rejected or aborted if the health status of a researcher's animals (e.g. presence of communicable animal diseases or parasites) may unduly jeopardize data acquired by other researchers.

Centre staff will provide expertise in monitoring the animal during the MRI scan, and can provide assistance with other animal procedures.  However, it may be necessary for the investigator to enlist his/her own animal technician if the procedures are beyond the scope of the Centre’s expertise.

A project is approved when:

  • the MRI Protocol Proposal and related amendments have been approved by the Protocol Committee
  • a valid ACC Protocol has been supplied for animal experiments
  • a satisfactory Animal Health Record has been supplied for animal experiments

All experiments must be scheduled through Centre staff (primary contact is Andrew Yung).  Scheduling is conducted on a first-come-first-serve basis but with some flexibility for those investigators with time-sensitive experiments.  In general, the scanner is available for use from 9AM to 6PM on weekdays, although there is some flexibility to this schedule.

The scan schedule can be checked by following this link.

Equipment entering the magnet room must be screened by Centre staff for magnetic compatibility.  If you intend to help with the study and enter the magnet room, you will be asked to complete a Safety Orientation and screening consultation.

Researchers are responsible for bringing their own animals from their animal housing facility to the scanner.  After any animal experiments, Centre staff will spray down exposed areas with Quatricide to minimize cross-contamination of other researchers’ experimental animals.

After every imaging session, the acquired data is archived on a mass storage unit accessible by internal network.

Once the experiment is finished, the data can be transferred to you by e-mail or CD if the dataset size is small.  If large amounts of data are generated or if regular access to data is required, then network access via SSH to the archived data can be arranged (please see the FAQ section).  Image data is available as TIFF, JPEG, or the native Bruker format.  The format and structure of the data that you receive is dependent on the naming and directory conventions that the scanner software uses (outlined in a pdf document that can be downloaded from the Resources page).

Centre staff are able to analyze the data generated by the MRI experiments according to the current fee schedule.  However, several software applications can be made available if you want to perform the analysis yourself.  We have a standalone Windows program suitable for basic image analysis and review, as well as various Matlab functions for reading and converting the data (go to the Documents and Downloads page in the Resources area).