Standard sequences @ 3T

Setting up an MRI protocol

A basic MR scan session usually starts with the following scans:

• Pre-scanning - a 3-plane localizer or 'scout' scan meant to find the subject's head. It is also be used for prescription for the subsequent scans. Doing some sort of localizer is necessary.
• Anatomical MRI - usually a 3D T1-weighted scan at 1mm isotropic resolution. It is essential for image alignment and anatomical analysis. More choices of anatomical scans are listed in the Anatomical imaging section.
• Shim - measures the magnetic field inhomogeneity and corrects it with polynomial gradients up to 2nd order. It should be run before fMRI or diffusion scans.

At this point you will want to add a number of functional scans, diffusion scans or other type of scans based on your experiment. In the next section we describe templates for different categories of MRI protocols. The protocol templates are organized by category.

You can get help in customizing the parameters from the Spinoza staff.

Anatomical MRI

1.0mm, TR=2000ms, FOV 256x2256x176mm, flip angle=8°, TR=7ms, TE= 3ms, RCS = 6 (AP), oversampling (RL) 1.28, for a total of 38 shots, and a duration of 1:55sec

Please cite "Stutters et al., Structural 3DT1 scans with compressed sensing are suitable for cross-sectional brain volume measures in multiple sclerosis. Proc Intl Soc Magn Reson Med 29(2021): 2150"

Classical BOLD fMRI

All with 10% gap, TE=27.63ms, SENSE 2, moderate PNS, maximum gradient mode, regular dynamic stabilization, 135Hz fat suppression SPIR offset, ascending slice order

3.0mm, TR=2000ms, FOV 240x240xxxxmm, WFS 12.0pix (36.0mm), Max dyns xxx (workhorse)
2.5mm, TR=3000ms, FOV 240x240xxxxmm, WFS 15.1pix (37.75mm), Max dyns xxx (high-res reduces signal drop out)

Multiband BOLD fMRI

All with 10% gap, TE=30ms, SENSE 1.5, multiband 4, moderate PNS, maximum gradient mode, regular dynamic stabilization, 175Hz fat suppression SPIR offset, ascending slice order
3.0mm, TR=0550ms, FOV 240x240x118mm, WFS 14.2pix (42.6mm), Max dyns 1820 (can be considered for denoising in people with increased heart rate)
2.7mm, TR=0700ms, FOV 240x240x130mm, WFS 14.4pix (38.9mm), Max dyns 1489 (workhorse)
2.0mm, TR=1600ms, FOV=224x224x125mm, WFS 23.7pix (47.4mm), Max dyns 1170 (high-res reduces signal drop out) 

Considerations:

Set shimbox to contain as little non-brain tissue and air as possible or use image based shimming through MRCode tool (requires image_based_shim patch)
Create second GE-EPI with opposite fatshift direction, set preparation to auto for this sequence (so it won't perform a second B0 shim) and group the sequences
Perhaps not include dummies and use one of the pre-saturation scans for registration as it has better grey/white matter contrast (see Multiband data registration)

GABA edited spectroscopy

We use a patch from Richard Edden (John's Hopkins University), which contains a MEGA-PRESS sequence for 3T. For more information on the development of this patch, see: www.gabamrs.com.

Please visit this website first for an explanation of the method used, before you start your experiment.

If you have any remaining questions after reading this Wiki page, please contact Anouk Schrantee.

The patch

The patch needs to be loaded with Select Patch and is currently called R5_4 MEGA. Please make sure you read the instructions on the do's and don't's of using patches here.

<to be inserted: photo how to select the correct patch>

How to acquire GABA data

There are currently two implementations to scan GABA working on the 3T.

- GABA_68_PAR: without macromolecule suppression

- GABA_80_PAR: with macromolecule suppression

The HERMES implementation is not yet working.

The analysis software

The developers of the patch also provide an analysis toolbox to analyze your spectroscopy data. For more information on this, and examples, please see: www.gabamrs.com. It exists of a series of Matlab scripts, but it can easily be called from the command line in Matlab - no need to change the scripts for the standard implementation. The manual of how to analyze your data is also in the folder mentioned below.

Important: You can download Gannet on their website, but we have optimized the analysis toolbox for the data that we acquire at the Spinoza, so please use the version you can find here: Gannet 2.0