pydesigner-v10-pythonic-implementation-designer-pipeline-for

PyDesigner v1.0: A Pythonic Implementation of the DESIGNER Pipeline for Diffusion Magnetic Resonance Imaging

PyDesigner is a Python-based software package based on the original Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) pipeline (Dv1) ...

New York University School of Medicine

We introduce and evaluate a post-processing technique for fast denoising of diffusion-weighted MR images. By exploiting the intrinsic redundancy in diffusion MRI using universal properties of the eigenspectrum of random covariance matrices, we remove noise-only principal components, thereby enabling signal-to-noise ratio enhancements. This yields parameter maps of improved quality for visual, quantitative, and statistical interpretation. By studying statistics of residuals, we demonstrate that the technique suppresses local signal fluctuations that solely originate from thermal noise rather than from other sources such as anatomical detail. Furthermore, we achieve improved precision in the estimation of diffusion parameters and fiber orientations in the human brain without compromising the accuracy and spatial resolution.

Denoising of diffusion MRI using random matrix theory.

Purpose To assess the diagnostic performance of the callosal angle (CA) and Evans index (EI) measures and to determine their role versus automated volumetric methods in clinical radiology. Materials and Methods Magnetic resonance (MR) examinations performed before surgery (within 1-5 months of the MR examination) in 36 shunt-responsive patients with normal-pressure hydrocephalus (NPH; mean age, 75 years; age range, 58-87 years; 26 men, 10 women) and MR examinations of age- and sex-matched patients with Alzheimer disease (n = 34) and healthy control volunteers (n = 36) were studied. Three blinded observers independently measured EI and CA for each patient. Volumetric segmentation of global gray matter, white matter, ventricles, and hippocampi was performed by using software. These measures were tested by using multivariable logistic regression models to determine which combination of metrics is most accurate in diagnosis. Results The model that used CA and EI demonstrated 89.6%-93.4% accuracy and average area under the curve of 0.96 in differentiating patients with NPH from patients without NPH (ie, Alzheimer disease and healthy control). The regression model that used volumetric predictors of gray matter and white matter was 94.3% accurate. Conclusion CA and EI may serve as a screening tool to help the radiologist differentiate patients with NPH from patients without NPH, which would allow for designation of patients for further volumetric assessment.  RSNA, 2017.

Diagnosis of Normal-Pressure Hydrocephalus: Use of Traditional Measures in the Era of Volumetric MR Imaging.

This work evaluates the accuracy and precision of the Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) pipeline, developed to identify and minimize common sources of methodological variability including: thermal noise, Gibbs ringing artifacts, Rician bias, EPI and eddy current induced spatial distortions, and motion-related artifacts. Following this processing pipeline, iterative parameter estimation techniques were used to derive diffusion parameters of interest based on the diffusion tensor and kurtosis tensor. We evaluated accuracy using a software phantom based on 36 diffusion datasets from the Human Connectome project and tested the precision by analyzing data from 30 healthy volunteers scanned three times within one week. Preprocessing with both DESIGNER or a standard pipeline based on smoothing (instead of noise removal) improved parameter precision by up to a factor of 2 compared to preprocessing with motion correction alone. When evaluating accuracy, we report average decreases in bias (deviation from simulated parameters) over all included regions for fractional anisotropy, mean diffusivity, mean kurtosis, and axonal water fraction of 9.7%, 8.7%, 4.2%, and 7.6% using DESIGNER compared to the standard pipeline, demonstrating that preprocessing with DESIGNER improves accuracy compared to other processing methods.

Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline.

At very low diffusion weighting the diffusion MRI signal is affected by intravoxel incoherent motion (IVIM) caused by dephasing of magnetization due to incoherent blood flow in capillaries or other sources of microcirculation. While IVIM measurements at low diffusion weightings have been frequently used to investigate perfusion in the body as well as in malignant tissue, the effect and origin of IVIM in normal brain tissue is not completely established. We investigated the IVIM effect on the brain diffusion MRI signal in a cohort of 137 radiologically-normal patients (62 male; mean age = 50.2 ± 17.8, range = 18 to 94). We compared the diffusion tensor parameters estimated from a mono-exponential fit at b = 0 and 1000 s/mm versus at b = 250 and 1000 s/mm. The asymptotic fitting method allowed for quantitative assessment of the IVIM signal fraction f* in specific brain tissue and regions. Our results show a mean (median) percent difference in the mean diffusivity of about 4.5 (4.9)% in white matter (WM), about 7.8 (8.7)% in cortical gray matter (GM), and 4.3 (4.2)% in thalamus. Corresponding perfusion fraction f* was estimated to be 0.033 (0.032) in WM, 0.066 (0.065) in cortical GM, and 0.033 (0.030) in the thalamus. The effect of f* with respect to age was found to be significant in cortical GM (Pearson correlation ρ ​= ​0.35, p ​= ​3*10) and the thalamus (Pearson correlation ρ = 0.20, p = 0.022) with an average increase in f* of 5.17*10/year and 3.61*10/year, respectively. Significant correlations between f* and age were not observed for WM, and corollary analysis revealed no effect of gender on f*. Possible origins of the IVIM effect in normal brain tissue are discussed.

Effect of intravoxel incoherent motion on diffusion parameters in normal brain.

Beta amyloid (Aβ) accumulation is the earliest pathological marker of Alzheimer's disease (AD), but early AD pathology also affects white matter (WM) integrity. We performed a cross-sectional study including 44 subjects (23 healthy controls and 21 mild cognitive impairment or early AD patients) who underwent simultaneous PET-MR using 18F-Florbetapir, and were categorized into 3 groups based on Aβ burden: Aβ- [mean mSUVr ≤1.00], Aβi [1.00 < mSUVr <1.17], Aβ+ [mSUVr ≥1.17]. Intergroup comparisons of diffusion MRI metrics revealed significant differences across multiple WM tracts. Aβi group displayed more restricted diffusion (higher fractional anisotropy, radial kurtosis, axonal water fraction, and lower radial diffusivity) than both Aβ- and Aβ+ groups. This nonmonotonic trend was confirmed by significant continuous correlations between mSUVr and diffusion metrics going in opposite direction for 2 cohorts: pooled Aβ-/Aβi and pooled Aβi/Aβ+. The transient period of increased diffusion restriction may be due to inflammation that accompanies rising Aβ burden. In the later stages of Aβ accumulation, neurodegeneration is the predominant factor affecting diffusion.

Diffusion MRI biomarkers of white matter microstructure vary nonmonotonically with increasing cerebral amyloid deposition.

To develop and evaluate a neural network-based method for Gibbs artifact and noise removal.

Training a neural network for Gibbs and noise removal in diffusion MRI.

Background Functional MRI improves preoperative planning in patients with brain tumors, but task-correlated signal intensity changes are only 2%-3% above baseline. This makes accurate functional mapping challenging. Marchenko-Pastur principal component analysis (MP-PCA) provides a novel strategy to separate functional MRI signal from noise without requiring user input or prior data representation. Purpose To determine whether MP-PCA denoising improves activation magnitude for task-based functional MRI language mapping in patients with brain tumors. Materials and Methods In this Health Insurance Portability and Accountability Act-compliant study, MP-PCA performance was first evaluated by using simulated functional MRI data with a known ground truth. Right-handed, left-language-dominant patients with brain tumors who successfully performed verb generation, sentence completion, and finger tapping functional MRI tasks were retrospectively identified between January 2017 and August 2018. On the group level, for each task, histograms of  scores for original and MP-PCA denoised data were extracted from relevant regions and contralateral homologs were seeded by a neuroradiologist blinded to functional MRI findings.  scores were compared with paired two-sided  tests, and distributions were compared with effect size measurements and the Kolmogorov-Smirnov test. The number of voxels with a  score greater than 3 was used to measure task sensitivity relative to task duration. Results Twenty-three patients (mean age ± standard deviation, 43 years ± 18; 13 women) were evaluated. MP-PCA denoising led to a higher median  score of task-based functional MRI voxel activation in left hemisphere cortical regions for verb generation (from 3.8 ± 1.0 to 4.5 ± 1.4;  < .001), sentence completion (from 3.7 ± 1.0 to 4.3 ± 1.4;  < .001), and finger tapping (from 6.9 ± 2.4 to 7.9 ± 2.9;  < .001). Median  scores did not improve in contralateral homolog regions for verb generation (from -2.7 ± 0.54 to -2.5 ± 0.40;  = .90), sentence completion (from -2.3 ± 0.21 to -2.4 ± 0.37;  = .39), or finger tapping (from -2.3 ± 1.20 to -2.7 ± 1.40;  = .07). Individual functional MRI task durations could be truncated by at least 40% after MP-PCA without degradation of clinically relevant correlations between functional cortex and functional MRI tasks. Conclusion Denoising with Marchenko-Pastur principal component analysis led to higher task correlations in relevant cortical regions during functional MRI language mapping in patients with brain tumors. © RSNA, 2020 

Improved Task-based Functional MRI Language Mapping in Patients with Brain Tumors through Marchenko-Pastur Principal Component Analysis Denoising.

Myelin insulates neuronal axons and enables fast signal transmission, constituting a key component of brain development, aging and disease. Yet, myelin-specific imaging of macroscopic samples remains a challenge. Here, we exploit myelin's nanostructural periodicity, and use small-angle X-ray scattering tensor tomography (SAXS-TT) to simultaneously quantify myelin levels, nanostructural integrity and axon orientations in nervous tissue. Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples. Outcomes are validated by 2D/3D histology and compared to MRI measurements sensitive to myelin and axon orientations. Specificity to nanostructure is exemplified by concomitantly imaging different myelin types with distinct periodicities. Finally, we illustrate the method's sensitivity towards myelin-related diseases by quantifying myelin alterations in dysmyelinated mouse brain. This non-destructive, stain-free molecular imaging approach enables quantitative studies of myelination within and across samples during development, aging, disease and treatment, and is applicable to other ordered biomolecules or nanostructures.

Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue.

Estimating intra- and extra-axonal microstructure parameters, such as volume fractions and diffusivities, has been one of the major efforts in brain microstructure imaging with MRI. The Standard Model (SM) of diffusion in white matter has unified various modeling approaches based on impermeable narrow cylinders embedded in locally anisotropic extra-axonal space. However, estimating the SM parameters from a set of conventional diffusion MRI (dMRI) measurements is ill-conditioned. Multidimensional dMRI helps resolve the estimation degeneracies, but there remains a need for clinically feasible acquisitions that yield robust parameter maps. Here we find optimal multidimensional protocols by minimizing the mean-squared error of machine learning-based SM parameter estimates for two 3T scanners with corresponding gradient strengths of 40and80mT/m. We assess intra-scanner and inter-scanner repeatability for 15-minute optimal protocols by scanning 20 healthy volunteers twice on both scanners. The coefficients of variation all SM parameters except free water fraction are ≲10% voxelwise and 1-4% for their region-averaged values. As the achieved SM reproducibility outcomes are similar to those of conventional diffusion tensor imaging, our results enable robust in vivo mapping of white matter microstructure in neuroscience research and in the clinic.

Article	Year
Denoising of diffusion MRI using random matrix theory. NeuroImage\| PubMed ID: 27523449	2016
Diagnosis of Normal-Pressure Hydrocephalus: Use of Traditional Measures in the Era of Volumetric MR Imaging. Radiology\| PubMed ID: 28498794	2017
Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline. NeuroImage\| PubMed ID: 30077743	2018
Effect of intravoxel incoherent motion on diffusion parameters in normal brain. NeuroImage\| PubMed ID: 31580945	2020
Diffusion MRI biomarkers of white matter microstructure vary nonmonotonically with increasing cerebral amyloid deposition. Neurobiology of aging\| PubMed ID: 32111392	2020
Training a neural network for Gibbs and noise removal in diffusion MRI. Magnetic resonance in medicine\| PubMed ID: 32662910	2021
Improved Task-based Functional MRI Language Mapping in Patients with Brain Tumors through Marchenko-Pastur Principal Component Analysis Denoising. Radiology\| PubMed ID: 33289611	2021
Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue. Nature communications\| PubMed ID: 34011929	2021
Reproducibility of the Standard Model of diffusion in white matter on clinical MRI systems. NeuroImage\| PubMed ID: 35545197	2022

Benjamin Ades-Aron

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