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) for dMRI preprocessing and tensor estimation. This software is openly provided for non-commercial research and may not be used for clinical care. PyDesigner combines tools from FSL and MRtrix3 to perform denoising, Gibbs ringing correction, eddy current motion correction, brain masking, image smoothing, and Rician bias correction to optimize the estimation of multiple diffusion measures.

Higher Dose Noninvasive Transcutaneous Auricular Vagus Nerve Stimulation Increases Feeding Volumes and White Matter Microstructural Complexity in Open-Label Study of Infants Slated for Gastrostomy Tube.

Objective: To determine whether transcutaneous auricular vagus nerve stimulation (taVNS) paired with twice daily bottle feeding increases the volume of oral feeds and white matter neuroplasticity in term-age-equivalent infants failing oral feeds and determined to need a gastrostomy tube.

Study Design: In this prospective, open-label study, 21 infants received taVNS paired with 2 bottle feeds for 2 - 3 weeks (2x). We compared 1) increase oral feeding volumes with 2x taVNS and previously reported once daily taVNS (1x) to determine a dose response, 2) number of infants who attained full oral feeding volumes, and 3) diffusional kurtosis imaging and magnetic resonance spectroscopy before and after treatment by paired t tests.

Optimized rectification of fiber orientation density function with background threshold.

Purpose: To describe an optimized fiber orientation density function (fODF) rectification procedure that removes negative values and absorbs all features below a specified threshold into a constant background.

Theory And Methods: The fODF for a white matter imaging voxel describes the angular density of axons. Because of signal noise and Gibbs ringing, fODFs estimated with diffusion MRI may take on unphysical negative values in some directions and contain spurious peaks.

Fiber Ball White Matter Modeling Reveals Microstructural Alterations in Healthy Brain Aging.

Age-related white matter degeneration is characterized by myelin breakdown and neuronal fiber loss that preferentially occur in regions that myelinate later in development. Conventional diffusion MRI (dMRI) has demonstrated age-related increases in diffusivity but provide limited information regarding the tissue-specific changes driving these effects. A recently developed dMRI biophysical modeling technique, Fiber Ball White Matter (FBWM) modeling, offers enhanced biological interpretability by estimating microstructural properties specific to the intra-axonal and extra-axonal spaces.

Transcutaneous auricular vagus nerve stimulation (taVNS) given for poor feeding in at-risk infants also improves their motor abilities.

Purpose: Transcutaneous auricular vagus nerve stimulation (taVNS) is a non-invasive neuromodulation technique that may improve oromotor skills when paired with feeding in at-risk infants, but effects on other motor function and how motor function relates to white matter (WM) microstructure are unknown.

Methods: In this prospective study, infants failing oral feeds and slated for gastrostomy tube (G-tube) placement received taVNS paired with bottle feeding daily for 2-3 weeks. The effects of taVNS-paired feeding on general and specific head movements were investigated using the Specific Test of Early infant motor Performance (STEP) and diffusion MRI obtained before and after taVNS treatment.

NAC and Vitamin D Improve CNS and Plasma Oxidative Stress in Neonatal HIE and Are Associated with Favorable Long-Term Outcomes.

N-acetylcysteine (NAC) and vitamin D provide effective neuroprotection in animal models of severe or inflammation-sensitized hypoxic ischemic encephalopathy (HIE). To translate these FDA-approved drugs to HIE neonates, we conducted an early phase, open-label trial of 10 days of NAC (25, 40 mg/kg q12h) + 1,25(OH)D (calcitriol 0.05 mg/kg q12h, 0.

High fidelity fiber orientation density functions from fiber ball imaging.

The fiber orientation density function (fODF) in white matter is a primary physical quantity that can be estimated with diffusion MRI. It has often been employed for fiber tracking and microstructural modeling. Requirements for the construction of high fidelity fODFs, in the sense of having good angular resolution, adequate data to avoid sampling errors, and minimal noise artifacts, are described for fODFs calculated with fiber ball imaging.

NAC and Vitamin D Restore CNS Glutathione in Endotoxin-Sensitized Neonatal Hypoxic-Ischemic Rats.

Therapeutic hypothermia does not improve outcomes in neonatal hypoxia ischemia (HI) complicated by perinatal infection, due to well-described, pre-existing oxidative stress and neuroinflammation that shorten the therapeutic window. For effective neuroprotection post-injury, we must first define and then target CNS metabolomic changes immediately after endotoxin-sensitized HI (LPS-HI). We hypothesized that LPS-HI would acutely deplete reduced glutathione (GSH), indicating overwhelming oxidative stress in spite of hypothermia treatment in neonatal rats.

Optimized rectification of fiber orientation density function.

Purpose: To demonstrate an optimized rectification strategy for fiber orientation density functions (fODFs).

Theory And Methods: In white matter, fODFs can be estimated with diffusion MRI. However, because of signal noise, imaging artifacts and other factors, experimentally determined fODFs may take on unphysical negative values in some directions.

N-acetylcysteine mitigates acute opioid withdrawal behaviors and CNS oxidative stress in neonatal rats.

Background: Neonatal abstinence syndrome (NAS) is a significant problem. Opioid withdrawal induces oxidative stress and disrupts glutamate and glutathione homeostasis. We hypothesized that N-acetylcysteine (NAC) administered during acute opioid withdrawal in neonatal rats would decrease withdrawal behaviors and normalize CNS glutathione and glutamate.

Triple diffusion encoding MRI predicts intra-axonal and extra-axonal diffusion tensors in white matter.

Purpose: To demonstrate how triple diffusion encoding (TDE) MRI can be applied to separately estimate the intra-axonal and extra-axonal diffusion tensors in white matter (WM).

Methods: Using a TDE pulse sequence with an axially symmetric b-matrix, diffusion MRI data were acquired at 3T for 3 healthy adults with an axial b-value of 4000 s/mm , a radial b-value of 307 s/mm , and 64 diffusion encoding directions. This acquisition was then repeated with the radial b-value set to 0.

Optimization of data acquisition and analysis for fiber ball imaging.

The inverse Funk transform of high angular resolution diffusion imaging (HARDI) data provides an estimate for the fiber orientation density function (fODF) in white matter (WM). Since the inverse Funk transform is a straightforward linear transformation, this technique, referred to as fiber ball imaging (FBI), offers a practical means of calculating the fODF that avoids the need for a response function or nonlinear numerical fitting. Nevertheless, the accuracy of FBI depends on both the choice of b-value and the number of diffusion-encoding directions used to acquire the HARDI data.

Identifying the translational complexity of magnetic resonance spectroscopy in neonates and infants.

Little attention has been paid to relating MRS outputs of vendor-supplied platforms to those from research software. This comparison is crucial to advance MRS as a clinical prognostic tool for disease or injury, recovery, and outcome. The work presented here investigates the agreement between metabolic ratios reported from vendor-provided and LCModel fitting algorithms using MRS data obtained on Siemens 3 T TIM Trio and 3 T Skyra MRI scanners in a total of 55 premature infants and term neonates with hypoxic ischemic encephalopathy (HIE).

N-Acetylcysteine rapidly replenishes central nervous system glutathione measured via magnetic resonance spectroscopy in human neonates with hypoxic-ischemic encephalopathy.

Persistent oxidative stress depletes reduced glutathione (GSH), an intracellular antioxidant and an important determinant of CNS injury after hypoxia ischemia. We used standard, short echo time Stimulated Echo Acquisition Mode (STEAM) to detect GSH by magnetic resonance spectroscopy (MRS) in 24 term neonates with hypoxic-ischemic encephalopathy (HIE), on day of life 5-6, after rewarming from therapeutic hypothermia. MRS demonstrated reliable, consistent GSH of 1·64 ± 0·20 mM in the basal ganglia immediately before intravenous infusion of N-acetylcysteine.