Emma Dixon1, Anna Barnes2, and Karin Shmueli1
1Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom, 2Institute of Nuclear Medicine, UCLH-NHS Foundation Trust, London, United Kingdom
Synopsis
Magnetic susceptibility mapping has the potential to facilitate segmentation of air and teeth in the head due to their different magnetic susceptibilities, though there is no phase signal in these regions. An iterative phase replacement method to
improve the calculation of susceptibility distributions in regions with no
phase signal is validated using a numerical phantom consisting of three classes: air, teeth and tissue with the phase image set to zero in the air and teeth to simulate the real case. Calculated susceptibility distributions in regions with no phase signal were not accurate and standard deviations were seen to increase in some regions, though
the iterative technique improved a simple segmentation.Purpose
Quantitative
Susceptibility Mapping (QSM) calculates the relative magnetic susceptibility (χ)
of tissues from the MRI phase data. In standard gradient-echo sequences there
is no phase signal for air, teeth and bone. However, due to
the non-local relationship between χ and phase, the phase
generated from these regions extends into adjacent regions with MR signal. This
phase information can be exploited to provide information about the χ of
regions with no phase signal. Here we assess an iterative phase replacement
(IPR) method proposed by Buch et. al. [1] using a numerical head phantom in
which we attempt to calculate the χ distribution in the air-filled sinuses and
teeth in order to segment these regions.
Methods
We
applied the IPR method [1] to a numerical χ phantom (figure 1a) modified from
that provided by Buch et al. by downsampling and removing χ variation within soft tissue. The phantom consisted of 3 classes: air (+9 ppm),
soft tissue (+0.09 ppm) and teeth (-3 ppm) [2]. The phase was calculated using
the forward model [3] with TE= 2.5 ms and B
0 = 3 T, setting the dipole kernel to 0 at
k=0. The
matrix size was 256
3, zero-padded to 512
3 and the voxels
were isotropic (1x1x1 mm
3).
B
0 was set along the inferior-posterior direction. The
phase in teeth and air was nulled to simulate the real case and IPR was applied as in [1]. As we found the change in χ to increase between successive iterations in some regions, 8 iterations were used rather than a stopping criterion based on the change in mean χ falling below an appropriate level in a chosen Region of Interest (ROI). Final χ maps (figures 1b-c) were calculated using threshold-based
k-space division (TKD) [4], with a threshold of 0.1 [1]; 0.4 and $$$\frac{2}{3}$$$ were also investigated. The mean and standard deviation (SD) of χ were recorded in several ROIs. The
ROIs were the air and teeth regions in the head as defined in the initial χ map and
single-slice sinus regions as shown in figures 1d-f. To assess the ability of IPR to improve
the segmentation of the regions with no phase signal into air, teeth and tissue, Otsu’s method was performed after each iteration to find a χ threshold between air and teeth [5], as tissue had previously been identified by thresholding the magnitude image.
Results
Results
from the IPR method over successive iterations are shown for the air, teeth and sinus ROIs. The final χ map for TKD threshold 0.1 is shown in figures 1b-c. Figures 2, 3 and 4 show that in the teeth the mean χ decreases and in the air/sinus regions the mean χ increases over iterations,
however the χ the iteration converges towards is different for
each region and each TKD threshold. The SD behaves differently depending on the region and TKD threshold. Figure 5 demonstrates the performance of the segmentation algorithm on the χ map (TKD threshold 0.1) at the end of each
iteration.
Discussion
In
common with the findings of Buch et. al [1], the first iteration of IPR produced the largest change in χ. However, convergence was not achieved within a small number of iterations meaning the stopping criterion was not applicable [1]. Calculated χ distributions were highly dependent on ROI geometry as can be seen from the different results obtained for three sinus regions, despite identical initial χ values. The SD did not
behave uniformly across regions and TKD thresholds, and increased in some regions,
suggesting that the repeated use of the regularized inverse calculation leads
to an increase in error. Mean χ values decreased as the TKD threshold increased as expected due to systematic underestimation which could be corrected as described in [6]. Despite inaccurate χ distributions, this method showed promise in aiding
automatic segmentation of air and teeth as shown in figure 5 where the first few iterations improve the segmentation. There were, however, regions which were misclassified, for example the pharynx, potentially due to alignment with the B
0 field or
adjacency with the image edge.
Conclusion
As it failed to converge on the correct χ value, IPR may not be
suitable for calculating accurate χ distributions in regions that have
no phase signal. However, IPR was found to aid a simple segmentation method in
distinguishing between air and teeth. Due to dependence on geometry, complex regions such as the mastoid sinus which
contains a mixture of air and bone may be particularly difficult to segment. Work is ongoing to investigate alternative inverse problem solutions for the susceptibility calculation.
Acknowledgements
We thank Sagar Buch for kindly providing the numerical phantom and assistance with the phase replacement method.References
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