Elisa Scaccianoce1,2, Francesca Baglio2, Giuseppe Baselli1, and Flavio Dell'Acqua3
1Department of Electrinics, Informations and Bioengineering, Politecnico di Milano, Milano, Italy, 2RM Lab, Don Carlo Gnocchi Foundation ONLUS, IRCCS S. Maria Nascente, Milano, Milano, Italy, 3NATBRAINLAB, Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, United Kingdom, London, United Kingdom
Synopsis
HARDI
datasets are often prone to different type of artifacts, difficult to detect
even by expert users. In this work we propose a fast and effective pipeline for
outlier identification and correction of HARDI datasets. Here corrupted data is first identified
as outlier and then regenerated using a framework based on signal decomposition
using spherical harmonics. This approach
was tested on healthy controls and validated with simulated dataset. Our study confirms
the efficacy of using SH for artifacts identification and correction. Background and purpose
High Angular Resolution
Diffusion Imaging (HARDI) is currently considered one of the most suitable
approach for study white matter connectivity and is routinely adopted in
several clinical research studies. However, with HARDI, a big amount of raw data
is also collected, making difficult to manually inspect all of Diffusion
Weighted (DW) volumes for artefacts that may negatively impact further
analyses. These artifacts, due to head movements, physiological noise and
scanner-related issue, are often also subtle and arduous to detect visually,
even by expert users. Tools for artifacts identification, based on the
evaluation of outliers when computing the residual of the signal fitted by
different models[1,2], have been already developed. However, these
methods detect outliers at the individual voxel level while most, if not all,
artifacts affecting HARDI data are usually impacting more voxels within the
same DW volume and brain slice. Moreover, most of this approaches simply reject
outliers and fit the specific diffusion model with the remaining data points
making potentially this estimation more computational demanding (i.e. applying a
customized b-matrix or fiber response model per each voxel). In this work we adopted
a fast slice-wise approach to detect corrupted slices within different DW
volumes and regenerate the missing data using spherical harmonics (SH)
decomposition of the HARDI signal. SH decomposition has also per se an
intrinsic beneficial effect of denoising and removal of any not antipodal
symmetric features of the HARDI signal. The final output is a fully regenerated
dataset that can be then processed with any existing diffusion pipeline.
Methods
HARDI data from 15 healthy
subjects, mean age 32 ± 5 years, were acquired using a 3T GE HDx system
(General Electric, Milwaukee, WI, USA) with the following parameters: voxel
size 2.4x2.4x2.4 mm, slices 60, b-value 3000 s/mm2, 60 diffusion-weighted
directions and 7 non-diffusion weighted volumes. After correcting for motion
and eddy current distortions using FSL (fsl.fmrib.ox.ac.uk/fsl), for each
subject the following steps were performed using a custom written Matlab code
(R2013a, www.mathworks.com): 1) HARDI data was fitted using a SH decomposition. 2)
Residuals values were computed as the difference between the actual HARDI signal
and the SH modelled signal. For each brain slice the mean value of this
residual was calculated along each DW direction. 3) A binary outlier mask was created
by identifying as outliers all DW directions with a mean residual value above an
automatic threshold obtained for each slice across all DW directions and
defined as: $$$threshold=Q3+IQR\times3$$$, where Q3 is the 75th percentile and
IQR is the interquartile range computed on the mean residuals[3]. 4)
Corrupted signals were regenerated using new SH coefficients obtained by SH
decomposition performed this time without outlier directions. SH at order 6 was
used when regenerating slices of corrupted directions while SH at order 8 was applied to the rest
of the data.
Results
To validate our method, a simulated artifact was created in a subject who did not present any artifact. In figure 1, panel a) shows the corrupted dataset in the sagittal view while panel b) displays the actual (left) and the regenerated (right) data. On real data, visual inspection of the diffusion dataset identified 2 subject with obvious and significant artefacts of along different DW directions. All artifacts were detected and corrected by the proposed approach. In figures 2 and 3, two examples of artifact correction are shown. Figure 2a illustrates the outlier mask in which one of the outlier value is identified and its location displayed in sagittal and axial views before (Fig. 2b) and after (Fig. 2c) correction. Similar results are show in figure 3. Few seconds were required to correct each subject on normal laptop.
Discussion and Conclusion
This work presents an effective and fast tool for the automatic outlier detection and correction. Our study confirms the efficacy of using SH for artifacts identification and proposes a completely model independent approach and simple solution for their correction. This approach can be useful in large studies when visual quality check may be not practical or when data artefacts are not obvious at visual inspection. To conclude, the present work introduces a fully automatic method for both artifact identification and correction of HARDI data which can potentially increase the precision in DW-derived measures.
Acknowledgements
No acknowledgement found.References
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