A diffusion-matched principal component analysis (DM-PCA) based two-channel denoising procedure for high-resolution diffusion-weighted MRI - Fig 4

<p>A simulation study for comparing magnitude-domain DM-PCA and two-channel complex-domain DM-PCA in terms of the accuracy in fitting ADC values from parallel DWI data: (a) Images reconstructed with the 2xSENSE algorithm from noise-free under-sampled k-space data corresponding to b = 0, 200, 400 … 2200 (s/mm²). (b) Images reconstructed with the 2xSENSE algorithm from noisy under-sampled k-space. (c) SENSE-produced data denoised by magnitude-domain DM-PCA. (d) SENSE-produced DWI data denoised by a two-channel complex-domain DM-PCA procedure. (e) Signal intensities of noisy parallel DWI data (solid curve in orange) and the ground truth (dashed curve in blue). (f) Signal intensities of magnitude-domain DM-PCA produced data (solid curve in orange) and the ground truth (dashed curve in blue). (g) Signal intensities of complex-domain DM-PCA produced data (solid curve in orange) and the ground truth (dashed curve in blue). (h) Errors in ADC fitting for data with different SNR levels.</p

Example anatomical MRI images of mice at early and late timepoints.

<p>Example high resolution T2-weighted in vivo images of <i>Npc1</i>^-/- (a-c, g-i) and WT (d-f, j-l) mice at 3 weeks (a-f) and 9 weeks (g-l) of age. At three weeks of age there are only slight differences between in the brains of <i>Npc1</i>^-/- and WT mice, but can be seen in the white matter regions of the brain. These differences become more pronounced at 9 weeks of age. The arrow in panel j points to the region of the corpus callosum and external capsule in a WT mouse, which demonstrates a dark band of intensity compared to the surrounding gray matter. This is reversed in the <i>Npc1</i>^-/- mouse. The cerebellum is circled in panel <i>k</i>, which is visibly reduced in size in the <i>Npc1</i>^-/- mouse at 9 weeks. The arrow in panel <i>l</i> indicates the bright signal of the CSF in the lateral ventricles, which are increased in size in the <i>Npc1</i>^-/- mouse at 9 weeks.</p

Example 9 week WT mouse images illustrating processing steps for volumetry analysis.

<p>Orthogonal views of the example T2-weighted in vivo dataset are shown in panel <i>a</i>. The images after semi-automated segmentation to remove signal from non-brain material are shown in panel <i>b</i>. The bias field estimate due to surface coil sensitivity inhomogeneity obtained from N4ITK software is shown in panel <i>c</i>. Panel <i>d</i> is the processed 3D dataset ready for image registration and analysis.</p

Change in the volume of mouse brain regions with age.

<p>Percent change in whole brain and brain region volumes between 3 and 9 months of age for WT (blue) and <i>Npc1</i>^-/- (red) mice. Errors bars indicate the standard deviation of the percent change. Significant effects of genotype (*) and age (*) and significant interaction between age and genotype (*) were determined from a two-way ANOVA and p<0.05 after Holm-Bonferroni correction.</p

A diffusion-matched principal component analysis (DM-PCA) based two-channel denoising procedure for high-resolution diffusion-weighted MRI - Fig 3

<p>A simulation study for comparing magnitude-domain DM-PCA and two-channel complex-domain DM-PCA in terms of the accuracy in ADC fitting: (a) Noise-free DWI data corresponding to b = 0, 200, 400 … 2200 (s/mm²). (b) DWI data affected by Rician noise. (c) DWI data denoised by magnitude-domain DM-PCA. (d) DWI data denoised by a two-channel complex-domain DM-PCA procedure. (e) Signal intensities of noisy DWI data (solid curve in orange) and the ground truth (dashed curve in blue). (f) Signal intensities of magnitude-domain DM-PCA produced data (solid curve in orange) and the ground truth (dashed curve in blue). (g) Signal intensities of complex-domain DM-PCA produced data (solid curve in orange) and the ground truth (dashed curve in blue). (h) Errors in ADC fitting for data with different SNR levels.</p

A diffusion-matched principal component analysis (DM-PCA) based two-channel denoising procedure for high-resolution diffusion-weighted MRI - Fig 2

<p>Comparison of DWI denoising through filtering signals across nearest neighboring voxels and diffusion-matched voxels: The red dot in (a) shows a target voxel (displayed on top of mean DWI map), whose signals in 6-direction DWI scans are to be denoised. In many existing denoising methods, signals of nearest neighboring voxels in a patch (see b) are the input of a filtering procedure. In contrast, we identify a group of voxels that demonstrate very similar signal variation patterns along the diffusion dimension but are not necessarily neighboring (see c) for subsequent filtering procedures. Panels d, e and f show an input image, nearest-neighboring PCA produced image, and DM-PCA produced image, respectively. Residual maps obtained with nearest-neighboring PCA and DM-PCA methods are shown in panels g and h, respectively.</p

The schematic diagram of the new complex-domain DM-PCA based two-channel denoising procedure.

<p>The schematic diagram of the new complex-domain DM-PCA based two-channel denoising procedure.</p

A diffusion-matched principal component analysis (DM-PCA) based two-channel denoising procedure for high-resolution diffusion-weighted MRI - Fig 7

<p>Application of DM-PCA denoising to human brain DWI data at conventional resolution (1.8 mm³ voxel size): Panels a and b compare one of the DWI images before and after DM-PCA denoising, respectively, for 4 of the participants. Panels c and d show the corresponding FA maps obtained from data before and after DM-PCA denoising, respectively.</p

A diffusion-matched principal component analysis (DM-PCA) based two-channel denoising procedure for high-resolution diffusion-weighted MRI - Fig 6

<p>(a) and (b) show coronal-plane mean DWI and FA maps, respectively, derived from high-resolution data after DM-PCA based denoising, with arrows indicating the left hippocampus. The corresponding zoom-in images shown in (c) and (d), respectively. The FA map derived from images without DM-PCA denoising is shown in (e). The coarse hippocampal structures revealed by the mean DWI map are highlighted in (f). Anatomic structures that can be identified from color-coded FA map are shown in (g) and (h). Region 1 in (g) corresponds to the dentate gyrus; Region 2 shows fibers that connect hippocampus and entorhinal cortex to other brain areas; Region 3 contains hippocampal CA1, CA2, and CA3.</p

Brain region volume^*, effects and interactions in 3 and 9 week old Npc1^-/- and control mice.

<p>Brain region volume^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178179#t001fn001" target="_blank">*</a>}, effects and interactions in 3 and 9 week old Npc1^-/- and control mice.</p