Martina F Callaghan1, Kerrin J Pine1, Karsten Tabelow2, Joerg Polzehl2, Nikolaus Weiskopf1,3, and Siawoosh Mohammadi1,4
1Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, London, United Kingdom, 2Weierstrass Institute, Berlin, Germany, 3Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, 4Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Synopsis
In vivo histology aims to
extract biologically relevant metrics from MRI data. In neuroimaging this
includes characterising white matter fibres in terms of orientation,
distribution and g-ratio, or determining the cortical myelo- and cyto-architecture.
It has been shown, both theoretically and experimentally, that the signal decay
in gradient recalled echoes (GRE) exhibits higher order temporal behaviour that
is dependent on a variety of intra-voxel microstructural metrics. Here we use
adaptive smoothing to generate maps of both the first and second order
components of the temporal decay of the GRE signal from short TE data using a
time-efficient multi-parameter mapping protocol.Purpose
The goal of in vivo
histology is to extract biologically relevant metrics from MRI data
1. In the neuroimaging domain this includes
characterising white matter fibres in terms of orientation, distribution and
g-ratio, or determining the myelo- and cyto-architecture within the cortex. This
task requires advanced biophysical models to relate the measured MRI signal to
the underlying tissue microstructure. It has previously been shown, through
theoretical modelling and experimental validation, that the signal decay in
gradient recalled echoes (GRE) exhibits higher order temporal behaviour
2 that is dependent on a variety of intra-voxel
microstructural metrics, e.g. fibre orientation, axonal and extra-cellular
volumes, compartment-specific susceptibility etc. The fact that such
biophysical models depend on an array of parameters makes their inversion to
extract biologically-relevant microstructural metrics ill-posed and
particularly problematic when dealing with noisy data. In addition, higher
order information is typically only accessible through the acquisition of long
TE data, leading to extended protocol durations. Here we use adaptive smoothing
to generate maps of both the first and second order components of the temporal
decay of the GRE signal from short TE (maximally 18.6ms) data using a time-efficient multi-parameter
mapping
3 (MPM) protocol.
Methods
Data were acquired on a 7T Magnetom
system (Siemens Healthcare, Germany) as part of a whole brain MPM protocol
3 with 800µm isotropic resolution. Multi-echo
spoiled gradient echo (SPGR) data were acquired with predominantly proton
density (PDw; flip angle = 6
0), T1- (29
0) or
magnetisation transfer (MTw; 6
0 plus a 4ms Gaussian pulse
2kHz off-resonance prior to excitation) weighting. Each had a TR of 25.5ms and echoes
were acquired with 2.3ms echo-spacing from TE = 2.5ms to TE = 14ms (MTw) or
18.6ms (PDw and T1w). The protocol duration was just under 25 minutes and additionally
provided data to generate quantitative maps of magnetisation transfer,
longitudinal relaxation rate and effective proton density (not shown here)
including correction of B
1+ inhomogeneity. Extending the ESTATICS approach
4, a common temporal decay with first
and second order components (orthogonalised with respect to each other) was
assumed for all contrasts, while allowing variable signal amplitude for each. This
was done twice: with and without adaptive smoothing of the weighted SPGR
volumes prior to the calculation of the decay components. The adaptive
smoothing aims to boost SNR while preserving anatomical boundaries, even on a
fine scale. This is achieved through a multi-scale smoothing procedure that
defines adaptive local weights to estimate a weighted signal average.
Results
Maps
of the first order component of the signal decay were of high quality, e.g.
figure 1A, B. The benefit of adaptive smoothing is primarily seen in the second
order component of the signal decay (figure 1: C versus D). As expected from
theoretical analysis
2, this second order component is higher in fibre
pathways that are orthogonal to the main field (figure 2). This can be seen by
comparing the map (figure 2C, D) with the corresponding fibre orientation
vectors derived from a diffusion weighted dataset (figure 2A, B) acquired from
the same participant in a different imaging session at 3T.
Conclusions
Adaptive smoothing improves
estimation of the second order component of the temporal decay of the GRE
signal. This allowed stable estimation of this component to be made from a time
efficient protocol with a maximum TE of just 18.6ms and a protocol duration of
just 25 minutes. The MPM protocol additionally provides further quantitative
information leading to a rich data set with which to investigate brain
microstructure. In agreement with theory, high values for the second order
component of the signal decay are seen in fibre pathways perpendicular to the
main field. Further understanding the microstructural components dominating
this higher order component of the GRE signal decay will be the focus of future
work.
Acknowledgements
The research leading to these results
has received funding from the European Research Council under the European
Union's Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement n°
616905. The Wellcome Trust Centre for Neuroimaging is supported by core funding
from the Wellcome Trust 0915/Z/10/Z.References
1. Weiskopf,
N., Mohammadi, S., Lutti, A. & Callaghan, M. F. Advances in MRI-based
computational neuroanatomy: from morphometry to in-vivo histology. Curr.
Opin. Neurol. 28, 313–22 (2015).
2. Wharton, S. & Bowtell, R.
Gradient echo based fiber orientation mapping using R2* and frequency
difference measurements. Neuroimage 83, 1011–23 (2013).
3. Weiskopf, N. et al.
Quantitative multi-parameter mapping of R1, PD*, MT, and R2* at 3T: a
multi-center validation. Front. Neurosci. 7, 1–11 (2013).
4. Weiskopf, N., Callaghan, M. F.,
Josephs, O., Lutti, A. & Mohammadi, S. Estimating the apparent transverse
relaxation time (R2*) from images with different contrasts (ESTATICS) reduces
motion artifacts. Front. Neurosci. 8, 1–10 (2014).