Wu et al. Using radiomic features to diagnose Parkinson’s disease
© Annals of Translational Medicine. All rights reserved. Ann Transl Med 2019 | http://dx.doi.org/10.21037/atm.2019.11.26
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out under standardized circumstances, i.e., in a quiet and
dimly lit room with minimal background noise and in a
resting state with the eyes open.
For each subject, the scanned PET image was first
spatially normalized to the Montreal Neurological Institute
(MNI) space (FDG-PET template) with linear and non-
linear 3D transformations, which made the image size and
resolution consistent. Next, the normalized PET images
were smoothed using a Gaussian smoothing kernel with
a full-width at half maximum (FWHM) value of 10×
10×10 mm
3
that
could blur image edges and improve the
signal-to-noise ratio. As a result, the preprocessed images
had a spatial resolution of 79×95×69 with a voxel size of
2×2×2 mm
3
.
Image data were preprocessed using Statistical Parametric
Mapping 12 (SPM12, Wellcome Department of Imaging
Neuroscience, Institute of Neurology, London, UK, http://
www.fil.ion.ucl.ac.uk/spm/) software implemented in
MATLAB R2018a (Mathworks Inc, Sherborn, MA, USA).
Denition of regions-of-interest
According to various previous studies, the morphological
and metabolic changes in some brain regions were directly
related to the pathology of PD. Metabolic changes in
relevant brain regions of PD patients have been detected
using
18
F-FDG PET (18,41). Therefore, we referred to
previous studies to select brain regions with morphological
and metabolic changes, including the superior frontal
(24,41,42), the middle frontal (24), supplementary motor
area (43), occipital gyrus (24), caudate nucleus (24,44),
putamen (42), pallidum (41), thalamus (24,41,42,44), inferior
temporal (24,44), cerebellum (24,41,42), and pons (45).
Figure 2 shows all the brain ROIs (n=95). We selected
90 regions from the anatomical automatic labeling (AAL)
template (46), and 5 other regions where functional imaging
studies in PD commonly report altered metabolism,
including bilateral cerebellum, bilateral pons and cerebellar
vermis.
To verify the effectiveness of above brain ROIs, we
further used a two-sample Student’s t-test in SPM12 for
group comparisons in Huashan cohort. In this step we set
the peak threshold to P<0.001 and performed family wise
error (FWE) correction throughout the brain region (35,47).
Radiomic features extraction
In this section, we extracted features by using the radiomics
tool developed by Vallieres et al. (https://github.com/
mvallieres/radiomics). We used “Texture Toolbox” in the
radiomics tool to perform texture analysis from each input
ROI. All steps were performed in MATLAB R2018a,
including wavelet band-pass ltering, isotropic resampling,
Lloyd-Max quantization, and feature calculation. Each
18
F-FDG PET image was prepared for intensity analysis,
matrix-based texture analysis, and wavelet analysis at a scale
of 2 mm. Firstly, the wavelet band-pass ltering was carried
out by applying different weights to bandpass sub-bands
(LHL, LHH, LLH, HLL, HHL, and HLH) of the volume
of interest (VOI), compared to low- and high-frequency
sub-bands (LLL and HHH) in the wavelet domain. The
ratio of the weight was defined by R, and the values of R
were 1/2, 2/3, 1 (no wavelet ltering), 3/2, and 2. Secondly,
isotropic resampling was performed at the initial in-plane
resolution of every PET image, the Lloyd-Max quantization
algorithm was applied to normalize the PET images to 256
gray-level images. Finally, we obtained four types of texture
matrices [gray-level co-occurrence matrix (GLCM), gray-
level run-length matrix (GLRLM), gray-level size zone
matrix (GLSZM), and neighborhood gray-tone difference
matrix (NGTDM)] from quantized PET images. Based on
above texture matrices, we achieved 43 texture features, 188
wavelet features and 4 intensity features. 43 texture features
include 3 histogram-based textures, 9 texture features from
the GLCM, 13 texture features from the GLRLM, 13
texture features from the GLSZM, 5 texture features from
the NGTDM. Four intensity features include SUV
max
,
SUV
peak
, SUV
mean
,
auc
CSH. Detailed radiomic features are
listed in Table 1.
Features selection
In order to reduce the number of features, we ensured
independence among features and only selected those
features that make an important contribution for the
classication step. In this step, the clinical basic information
(age and gender) was also added into the radiomic features.
A 5-fold cross-validation algorithm was carried out in this
procedure.
The feature selection step was performed through two
steps: feature autocorrelation and fisher score algorithm.
First, feature autocorrelation was performed to reduce
redundancy between high-dimensional features. For each
feature, the average absolute correlation based on pair-
wise correlations was calculated, as dened by the following
formula: