BrainImageJ: a Java-based framework for interoperability in neuroscience, with specific application to neuroimaging.

The Human Brain Project consortium continues to struggle with effective sharing of tools. To facilitate reuse of its tools, the Stanford Psychiatry Neuroimaging Laboratory (SPNL) has developed BrainImageJ, a new software framework in Java. The framework consists of two components-a set of four programming interfaces and an application front end. The four interfaces define extension pathways for new data models, file loaders and savers, algorithms, and visualization tools. Any Java class that implements one of these interfaces qualifies as a BrainImageJ plug-in-a self-contained tool. After automatically detecting and incorporating new plug-ins, the application front end transparently generates graphical user interfaces that provide access to plug-in functionality. New plug-ins interoperate with existing ones immediately through the front end. BrainImageJ is used at the Stanford Psychiatry Neuroimaging Laboratory to develop image-analysis algorithms and three-dimensional visualization tools. It is the goal of our development group that, once the framework is placed in the public domain, it will serve as an interlaboratory platform for designing, distributing, and using interoperable tools.

Reduced field-of-view diffusion imaging of the human spinal cord: comparison with conventional single-shot echo-planar imaging.

BACKGROUND AND PURPOSE: DWI of the spinal cord is challenging because of its small size and artifacts associated with the most commonly used clinical imaging method, SS-EPI. We evaluated the performance of rFOV spinal cord DWI and compared it with the routine fFOV SS-EPI in a clinical population. MATERIALS AND METHODS: Thirty-six clinical patients underwent 1.5T MR imaging examination that included rFOV SS-EPI DWI of the cervical spinal cord as well as 2 comparison diffusion sequences: fFOV SS-EPI DWI normalized for either image readout time (low-resolution fFOV) or spatial resolution (high-resolution fFOV). ADC maps were created and compared between the methods by using single-factor analysis of variance. Two neuroradiologists blinded to sequence type rated the 3 DWI methods, based on susceptibility artifacts, perceived spatial resolution, signal intensity-to-noise ratio, anatomic detail, and clinical utility. RESULTS: ADC values for the rFOV and both fFOV sequences were not statistically different (rFOV: 1.01 ± 0.18 × 10(-3) mm(2)/s; low-resolution fFOV: 1.12 ± 0.22 × 10(-3) mm(2)/s; high-resolution fFOV: 1.10 ± 0.21 × 10(-3) mm(2)/s; F = 2.747, P > .05). The neuroradiologist reviewers rated the rFOV diffusion images superior in terms of all assessed measures (P < 0.0001). Particular improvements were noted in patients with metal hardware, degenerative disease, or both. CONCLUSIONS: rFOV DWI of the spinal cord overcomes many of the problems associated with conventional fFOV SS-EPI and is feasible in a clinical population. From a clinical standpoint, images were deemed superior to those created by using standard fFOV methods.

Reduction of motion artifacts in cine MRI using variable-density spiral trajectories.

Dynamic cardiac imaging in MRI is a very challenging task. To obtain high spatial resolution, temporal resolution, and signal-to-noise ratio (SNR), single-shot imaging is not sufficient. Use of multishot techniques resolves this problem but can cause motion artifacts because of data inconsistencies between views. Motion artifacts can be reduced by signal averaging at some cost in increased scan time. However, for the same increase in scan time, other techniques can be more effective than simple averaging in reducing the artifacts. If most of the energy of the inconsistencies is limited to a certain region of kappa-space, increased sampling density (oversampling) in this region can be especially effective in reducing motion artifacts. In this work, several variable-density spiral trajectories are designed and tested. Their efficiencies for artifact reduction are evaluated in computer simulations and in scans of normal volunteers. The SNR compromise of these trajectories is also investigated. The authors conclude that variable-density spiral trajectories can effectively reduce motion artifacts with a small loss in SNR as compared with a uniform density counterpart.

Magnetic resonance velocity imaging using a fast spiral phase contrast sequence.

Time-resolved velocity imaging using the magnetic resonance phase contrast technique can provide clinically important quantitative flow measurements in vivo but suffers from long scan times when based on conventional spin-warp sequences. This can be particularly problematic when imaging regions of the abdomen and thorax because of respiratory motion. We present a rapid phase contrast sequence based on an interleaved spiral k-space data acquisition that permits time-resolved, three-direction velocity imaging within a breath-hold. Results of steady and pulsatile flow phantom experiments are presented, which indicate excellent agreement between our technique and through plane flow measurements made with an in-line ultrasound probe. Also shown are results of normal volunteer studies of the carotids, renal arteries, and heart.

Reconstructions of phase contrast, phased array multicoil data.

We present a reconstruction method for phased array multicoil data that is compatible with phase contrast MR angiography. The proposed algorithm can produce either complex difference or phase difference angiograms. Directional flow and quantitative information are preserved with the phase difference reconstruction. The proposed method is computationally efficient and avoids intercoil cancellation errors near the velocity aliasing boundary. Feasibility of the method is demonstrated on human scans.

Computing material-selective projection images in MR.

We detail a robust, general method for computing projection images of individual materials in a volume as linear combinations of MR projection images with different material-dependent weightings. Signal per unit volume for each material in each raw image is acquired directly for accurate cancellation of undesired, overlapping materials. The weighted sum of the input images is determined to maximize the signal-to-noise ratio (SNR) and minimize inhomogeneity effects in the material-selective images. We tested the implementation experimentally in both phantom and human studies, producing selective images with reasonable SNRs and material isolation. With further development of sequences to rapidly acquire input images having greater material differentiability, we envision the application of the selective projection imaging format to screening studies searching over large volumes for diseased tissues.

Quantitative magnetic resonance flow imaging.

Time-of-flight and phase shift methods have both been used for vascular imaging with magnetic resonance. Phase methods, and phase contrast in particular, are well suited to quantitative measurements of velocity and volume flow rate. The most robust methods for measuring flow encode through-plane velocity into phase shift and compute flow by integrating the measured velocity over the vessel lumen. The accuracy of the flow data can be degraded by the effects of acceleration and eddy currents and by partial volume effects, including the effects of finite slice thickness and resolution, pulsatile waveforms, motion, and chemical shift. The reproducibility depends on the signal-to-noise of the data and the strength of the flow encoding and can be degraded by inconsistent definition of the vessel boundary. The adjustable flow sensitivity inherent in this method is a particular asset, allowing phase contrast flow measurement to operate over a dynamic range exceeding 10(5). Recently developed rapid imaging methods are helpful in applications that would be compromised by respiratory motion. With care, excellent quantitative data can be quickly obtained in vivo, and the resulting flow information is valuable for the diagnosis and management of a variety of conditions.

Renal artery blood flow: quantitation with phase-contrast MR imaging with and without breath holding.

PURPOSE: To compare the accuracy of 16-frame cine phase-contrast (PC) magnetic resonance (MR) imaging with those of two breath-hold PC techniques in the measurement of renal artery blood flow. MATERIALS AND METHODS: In vitro flow measurements were performed in a segment of harvested human artery embedded in gel. For the cine PC acquisition, respiratory motion was simulated. In eight subjects with recently obtained para-amino-hippurate-clearance renal blood flow data, renal artery flow measurements were subsequently performed with two breath-hold imaging techniques and with cine PC imaging during shallow respiration. RESULTS: Breath-hold sequences were significantly more accurate than conventional cine PC sequences both in vitro (P < .005) and in vivo (P < .05). Cine PC imaging tended to overestimate flow (in vivo mean, 24.47% +/- 9.94), reflecting artifactual enlargement of the apparent vessel size. CONCLUSION: Reliable blood flow measurements in the renal artery are possible with breath-hold PC MR imaging.