Magnetic Resonance Imaging of Water Content and Flow Processes in Natural Soils by Pulse Sequences with Ultrashort Detection.

Magnetic resonance imaging is a valuable tool for three-dimensional mapping of soil water processes due to its sensitivity to the substance of interest: water. Since conventional gradient- or spin-echo based pulse sequences do not detect rapidly relaxing fractions of water in natural porous media with transverse relaxation times in the millisecond range, pulse sequences with ultrafast detection open a way out. In this work, we compare a spin-echo multislice pulse sequence with ultrashort (UTE) and zero-TE (ZTE) sequences for their suitability to map water content and its changes in 3D in natural soil materials. Longitudinal and transverse relaxation times were found in the ranges around 80 ms and 1 to 50 ms, respectively, so that the spin echo sequence misses larger fractions of water. In contrast, ZTE and UTE could detect all water, if the excitation and detection bandwidths were set sufficiently broad. More precisely, with ZTE we could map water contents down to 0.1 cm3/cm3. Finally, we employed ZTE to monitor the development of film flow in a natural soil core with high temporal resolution. This opens the route for further quantitative imaging of soil water processes.

Functional-structural root-system model validation using a soil MRI experiment.

For the first time, a functional-structural root-system model is validated by combining a tracer experiment monitored with magnetic resonance imaging and three-dimensional modeling of water and solute transport.

Effect of magnetic pore surface coating on the NMR relaxation and diffusion signal in quartz sand.

Magnetic impurities are ubiquitous in natural porous media such as sand and soil. They generate internal magnetic field gradients because of increased magnetic susceptibility differences between solid and liquid phase in the pore space and because of the presence of magnetic centers. These internal gradients accelerate NMR relaxation rates and thus might limit the possibility of pore space characterization using NMR. In this study, we investigate the effects of coating the surface of natural sands by the antiferromagnetic iron oxyhydroxide goethite on NMR relaxation and diffusion properties. We found a non-quadratic dependence of the relaxation time distributions on the echo time indicating that the relaxation experiments were not performed in the fast diffusion limit, while the weak dependence on the external magnetic field strength is explained by the preponderance of the surface relaxation over the effect of diffusion in internal gradients. The surface to volume ratio of the pore space, determined by NMR diffusimetry ((S/V)NMR ) remains approximately constant, whereas the same quantity, determined from gas adsorption ((S/V)BET ) increases proportional to the coating density. This is because gas adsorption measures surface roughness on sub-nanometer scale, whereas NMR diffusimetry averages over structures smaller than few microns. This has consequences for the calculation of the surface relaxivities. The usage of the (S/V)NMR leads to constant values, whereas the usage of (S/V)BET leads to apparently decreasing relaxivities with increasing coating, which is unrealistic. Copyright © 2016 John Wiley & Sons, Ltd.

3D U-Net Segmentation Improves Root System Reconstruction from 3D MRI Images in Automated and Manual Virtual Reality Work Flows.

Magnetic resonance imaging (MRI) is used to image root systems grown in opaque soil. However, reconstruction of root system architecture (RSA) from 3-dimensional (3D) MRI images is challenging. Low resolution and poor contrast-to-noise ratios (CNRs) hinder automated reconstruction. Hence, manual reconstruction is still widely used. Here, we evaluate a novel 2-step work flow for automated RSA reconstruction. In the first step, a 3D U-Net segments MRI images into root and soil in super-resolution. In the second step, an automated tracing algorithm reconstructs the root systems from the segmented images. We evaluated the merits of both steps for an MRI dataset of 8 lupine root systems, by comparing the automated reconstructions to manual reconstructions of unaltered and segmented MRI images derived with a novel virtual reality system. We found that the U-Net segmentation offers profound benefits in manual reconstruction: reconstruction speed was doubled (+97%) for images with low CNR and increased by 27% for images with high CNR. Reconstructed root lengths were increased by 20% and 3%, respectively. Therefore, we propose to use U-Net segmentation as a principal image preprocessing step in manual work flows. The root length derived by the tracing algorithm was lower than in both manual reconstruction methods, but segmentation allowed automated processing of otherwise not readily usable MRI images. Nonetheless, model-based functional root traits revealed similar hydraulic behavior of automated and manual reconstructions. Future studies will aim to establish a hybrid work flow that utilizes automated reconstructions as scaffolds that can be manually corrected.

Imaging water fluxes in porous media by magnetic resonance imaging using D(2)O as a tracer.

In this study, we investigate the usefulness of D(2)O as a conservative tracer for monitoring water flux by MRI in a heterogeneous sand column. The column consisted of a cylindrical 3x9-cm packing of fine sand in which an 8-mm diameter cylindrical obstacle was placed. Constant steady-state flux densities between J(w)=0.07 and 0.28 cm min(-1) corresponding to mean pore flow velocities between 0.20 and 0.79 cm min(-1) were imposed at the top of the sand column, and a constant hydraulic head of -39 cm was maintained at the lower boundary. We injected pulses of 0.01 M NiCl(2) and 55% D(2)O and monitored the motion of the tracer plumes by MRI using a fast spin echo sequence over a period of 20 min. We observed that the center of gravity of all plumes moved with the mean pore flow velocity, which showed that D(2)O behaves as a conservative tracer. The motion of the tracer plume at J(w)=0.14 cm min(-1) was validated by a numerical simulation using HYDRUS2D, which reproduced the experimentally observed behavior very satisfactorily.

NMR velocimetry with 13-interval stimulated echo multi-slice imaging in natural porous media under low flow rates.

Characterization and quantification of root water uptake processes play a key role in understanding and managing the effects of global climate change on agricultural production and ecosystem dynamics. Part of this understanding is related to the flow of water towards plant roots in soils. In this study we demonstrate for the first time, to our knowledge, that fluid flow in the voids of the pore space of a model soil system (natural sand) can be detected and mapped to an NMR image for mean flows as low as 0.06 mm/s even under the influence of internal magnetic field gradients. To accomplish this we combined multi-slice imaging with a 13-interval pulse sequence to the NMR pulse sequence 13-interval stimulated echo multi-slice imaging (13-interval STEMSI). The result is a largely reduced influence of the internal magnetic field gradients, leading to an improved signal-to-noise ratio which in turn enables one to acquire velocity maps where conventional stimulated echo methods fail.

Oxidation of ferrocyanide by birnessite.

The Fe-CN complexes ferrocyanide, [FeII(CN)6]4-, and ferricyanide, [FeIII(CN)6]3-, which are contaminants in soil and groundwater, form a redox couple, [FeII(CN)6]4- <==> [FeIII(CN)6]3- + e-, E(H) = 356 mV. We studied the oxidation of [FeII(CN)6]4- by birnessite, delta-MnIVO2, in batch experiments as influenced by [FeII(CN)6]4- concentration, pH, and reaction time. Additionally, stopped-flow experiments were carried out at five temperatures (10-30 degrees C) and four pH values (pH 4.1-5.3). In the batch experiments, [FeII(CN)6]4- was completely oxidized to [FeIII(CN)6]3-, and oxidation did neither depend on time for t > 2 min, nor on concentration (0.12-0.47 mM), nor on pH (pH 3.3-9.9). Lasting adsorption of Fe-CN complexes on the birnessite surface or precipitation of manganese ferricyanide were not detected. Manganous ions resulting from the reductive dissolution of birnessite did not precipitate as manganese oxide because an identical decrease of Mn solution concentrations was observed under air and under a N2 atmosphere. Two processes were detected by the stopped-flow experiments. The first rapid one with an activation energy of approximately 60 kJ mol(-1) was attributed to short-term adsorption and simultaneous oxidation of [FeII(CN)6]4- on the birnessite surface. The second slower process with an activation energy of approximately 20 kJ mol(-1) was attributed most probably to diffusion of the reaction product Mn2+ into the interior of the birnessite, which creates fresh reaction sites at the outer surface.