Standard sequences @ 3T: Difference between revisions
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*Perhaps not include dummies and use one of the pre-saturation scans for registration as it has better grey/white matter contrast (see [https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/registration/index.html#multiband Multiband data registration]) | *Perhaps not include dummies and use one of the pre-saturation scans for registration as it has better grey/white matter contrast (see [https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/registration/index.html#multiband Multiband data registration]) | ||
= | =Magnetic Resonance Spectroscopy= | ||
If you have questions about our standard MRS sequences (e.g. GABA, glutamate), please contact [mailto:a.g.schrantee@amsterdamumc.nl Anouk Schrantee]. | |||
Revision as of 15:40, 27 January 2022
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.
Pre-scanning
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 (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)
Magnetic Resonance Spectroscopy
If you have questions about our standard MRS sequences (e.g. GABA, glutamate), please contact Anouk Schrantee.