Choosing an MRI protocol for your experiment

May 5th, 2017
May 5th, 2017

The CNI’s Wiki pages offer general advice about how to set up your scan protocols and save the information for later use. The wiki pages take you through the template protocols we think are most widely used. These protocols can be found on the the scanner console, saved under “CNI/head” within the protocol pool.

The protocol templates are organized by category.  One set is based on conventional multislice (2D) or 3D methods, a second set is based on the new simultaneous multislice (SMS) protocols (also called mux or multiband), and a third set are some special methods (spectroscopy and qMRI).

We provide a variety of templates in each category and some recommendations about choosing the right template based on our experience. You can get help in customizing the parameters from the CNI staff (ask Hua, Adam, or Laima).

Here is a brief description of the templates.  All the protocols start with ‘CNI Example’.  The examples below show several ‘presets’ for different types of scans.  You can change the parameters in most cases.

  • CNI Example Anatomical  - A great opening item for most experiments
    • T1w (0.8/0.9/1 mm, sag/ax)
    • T2w (0.8 mm, sag, w/o FLAIR/PROMO)
    • T2w/PDw
  • CNI Example basic fMRI - The GE classic BOLD product sequence, a customer favorite
    • BOLD EPI full brain coverage (2.9mm)
    • BOLD EPI partial brain coverage (1.8mm)
  • CNI Example basic DWI
    • DTI (b=1000, dir=60) – If you plan to use a diffusion tensor model, this will do
    • HARDI (b=2000/2500, dir=80/96) – For more advanced models these parameters are better
  • CNI Example SMS fMRI – Prepared specially our CNI chefs, and now offered nationwide
    • BOLD EPI (mux=6/8, 2.4/2 mm) – BOLD imaging goes forth to SMS, locally grown
    • Multi-echo EPI (3 echoes) – Useful for looking at T2* in BOLD
  • CNI Example SMS DWI – If you are in a hurry for a nutritious scan
    • HARDI (b=2500/3000, dir=80/96)
    • Multi-shell (2-shell, 3-shell)
  • CNI Example qMR – For those devoted to quantification
    • T1 map (2mm)
    • T1 map + PD map (1mm)
  • CNI Example Spectroscopy – Laima’s secret sauce
    • IMSPECIAL (new GABA measurement)
    • Probe-P general (more metabolites)

If you would like to run a different protocol from the ones listed here, please contact us.  We can very likely help configure the protocol.  For example, we can help users who would like to run multi-shell DWI used by NODDI, or with other sequences.

Hua and Brian


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