Clinical Imaging Sciences Centre: imaging methods

The Scanners

Siemens Prisma

Whole-body scanner

Field Strength: 3 Tesla

Gradient strength: 80 mT/m

Siemens Avanto

Whole-body scanner

Field strength: 1.5 Tesla

Gradient strength: 44 mT/m

Magnetization Transfer Imaging

The signal in conventional MR imaging comes primarily from water within the body; it cannot detect signal directly from important macromolecular components such as myelin. However, through a specially designed Magnetization Transfer (MT) MRI acquisition sequence we can detect the transfer of magnetization from the water pool to the macromolecular pool. This can reveal information such as the size of the pool (i.e. to study demyelination) which is vital for a number of white matter diseases in the brain.

Magnetization transfer imaging comes in a number of different flavours depending on the time available, resolution and the information required:

Quantitative MT (qMT)

Total acquisition time: 10 minutes

Sequence: 3D balanced steady-state free precession

Matrix size: 256 x 96 x 32 (sagittal slice orientation)

Resolution:  0.94 x 1.9 x 5 mm

Volumes acquired: 22 (with flip angle varied 5-40°; pulse duration 0.2 – 2.5 ms)

Repetition time: 3.66-5.96 ms

Echo time (TE): 1.83-2.98 ms

Analysis: complex, requires pixelwise non-linear fitting with in-house software.

Example reference: Dowell et al (2016) Biol Psych 79:320-328

Magnetization Transfer Ratio (MTR)

Total acquisition time: 6 minutes

Sequence: 3D gradient echo

Matrix Size: 256 x 144 x 48 (sagittal slice orientation)

Resolution:  0.94 x 0.94 x 2.5 mm

Flip angle: 5°

Volumes acquired: 2 (MT pulse on; MT pulse off)

Repetition time: 30 ms

Echo time (TE): 5 ms

Analysis: simple; take ratio of pixel intensities.

Example reference: Cercignani et al (2006) Neuroimage 31(1):181-6

Diffusion-weighted imaging

Many tissues in the body have a well-defined microstructural organization; for example the axonal fibres of the white matter in the brain or spinal cord. Water diffuses through and around these structures and the pattern of this diffusion can be detected by a specially-designed MRI acquisition approach called diffusion-weighted imaging. A number of analysis models have been developed that can give specific microstructural parameters. For example, Neurite Orientation Dispersion and Density Imaging (NODDI) tell us about the distribution of white matter fibres and the neurite density in the brain. Diffusion tensor imaging (DTI) is a more simplistic model but can provide a map of diffusion coefficients across the brain, together with a summary measure of diffusion anisotropy.

NODDI

Acquisition time: 9 minutes

Sequence: diffusion-weighted echo planar imaging

Repetition time (TR): 3600 ms

Echo time (TE): 80 ms

Diffusion weighting: 64 directions (b=2600) and 30 directions (b=800)

Acceleration: multiband factor 2; GRAPPA 2.

Analysis: complex; voxelwise fitting with non-linear modelling with Matlab toolbox

Example reference: Dowell et al (2019) Neuroscience 403:111-117.

DTI

Acquisition time: 5 minutes

Sequence: diffusion-weighted echo planar imaging

Repetition time (TR): 3600 ms

Echo time (TE): 80 ms

diffusion weighting: 30 directions (b=1000)

Acceleration: multiband factor 2; GRAPPA 2.

Analysis: simple; diffusion tensor fitting with FSL

Magnetic Resonance Spectroscopy

The metabolites in the body can be detected using magnetic resonance spectroscopy (MRS). Each metabolite contributes a distinct number of peaks to the spectrum and so the relative concentrations of the metabolites can be determined.

Single Voxel Spectroscopy (SVS)

Acquisition time: 6 minutes

Sequence: PRESS

Repetition time (TR): 1500 ms

Echo time (TE): 30 ms

Flip angle: 90°

Averages: 256

Analysis: peak fitting using jMRUI and Tarquin