MR fingerprinting reconstruction with Kalman filter

Magnetic resonance fingerprinting (MR fingerprinting or MRF) is a newly introduced quantitative magnetic resonance imaging technique, which enables simultaneous multi-parameter mapping in a single acquisition with improved time efficiency. The current MRF reconstruction method is based on dictionary matching, which may be limited by the discrete and finite nature of the dictionary and the computational cost associated with dictionary construction, storage and matching.In this paper, we describe a reconstruction method based on Kalman filter for MRF, which avoids the use of dictionary to obtain continuous MR parameter measurements. With this Kalman filter framework, the Bloch equation of inversion-recovery balanced steady state free-precession (IR-bSSFP) MRF sequence was derived to predict signal evolution, and acquired signal was entered to update the prediction. The algorithm can gradually estimate the accurate MR parameters during the recursive calculation. Single pixel and numeric brain phantom simulation were implemented with Kalman filter and the results were compared with those from dictionary matching reconstruction algorithm to demonstrate the feasibility and assess the performance of Kalman filter algorithm.The results demonstrated that Kalman filter algorithm is applicable for MRF reconstruction, eliminating the need for a pre-define dictionary and obtaining continuous MR parameter in contrast to the dictionary matching algorithm.     

Algorithm comparison for schedule optimization in MR fingerprinting

In MR Fingerprinting, the flip angles and repetition times are chosen according to a pseudorandom schedule. In previous work, we have shown that maximizing the discrimination between different tissue types by optimizing the acquisition schedule allows reductions in the number of measurements required. The ideal optimization algorithm for this application remains unknown, however. In this work we examine several different optimization algorithms to determine the one best suited for optimizing MR Fingerprinting acquisition schedules.     

Simultaneous quantification of SPIO and gadolinium contrast agents using MR fingerprinting

PurposeDevelop a magnetic resonance fingerprinting (MRF) methodology with R₂¹ quantification, intended for use with simultaneous contrast agent concentration mapping, particularly gadolinium (Gd) and iron labelled CD8+ T cells.MethodsVariable-density spiral SSFP MRF was used, modified to allow variable TE, and with an exp.(−TE·R₂¹) dictionary modulation. In vitro phantoms containing SPIO labelled cells and/or gadolinium were used to validate parameter maps, probe undersampling capacity, and verify dual quantification capabilities. A C57BL/6 mouse was imaged using MRF to demonstrate acceptable in vivo resolution and signal at 8× undersampling necessary for a 25-min scan.ResultsStrong agreement was found between conventional and MRF-derived values for R₁, R₂, and R₂¹. Expanded MRF allowed quantification of iron-loaded CD8+ T cells. Results were robust to 8× undersampling and enabled recreation of relaxation profiles for both a Gd agent and iron labelled cells simultaneously. In vivo data demonstrated sufficient SNR in undersampled data for parameter mapping to visualise key features.ConclusionMRF can be expanded to include R₁, R₂, and R₂¹ mapping required for simultaneous quantification of gadolinium and SPIO in vitro, allowing for potential implementation of a variety of future in vivo studies using dual MR contrast agents, including molecular imaging of labelled cells.     

Feasibility of MR fingerprinting using a high-performance 0.55 T MRI system

BackgroundMR fingerprinting (MRF) is a versatile method for rapid multi-parametric quantification. The application of MRF for lower MRI field could enable multi-contrast imaging and improve exam efficiency on these systems. The purpose of this work is to demonstrate the feasibility of 3D whole-brain T1 and T2 mapping using MR fingerprinting on a contemporary 0.55 T MRI system.Materials and methodsA 3D whole brain stack-of-spirals FISP MRF sequence was implemented for 0.55 T. Quantification was validated using the NIST/ISMRM Quantitative MRI phantom, and T1 and T2 values of white matter, gray matter, and cerebrospinal fluid were measured in 19 healthy subjects. To assess MRF performance in the lower SNR regime of 0.55 T, measurement precision was calculated from 100 simulated pseudo-replicas of in vivo data and within-session measurement repeatability was evaluated.ResultsT1 and T2 values calculated by MRF were strongly correlated to standard measurements in the ISMRM/NIST MRI system phantom (R² > 0.99), with a small constant bias of approximately 5 ms in T2 values. 3D stack-of-spirals MRF was successfully applied for whole brain quantitative T1 and T2 at 0.55 T, with spatial resolution of 1.2 mm × 1.2 mm × 5 mm, and acquisition time of 8.5 min. Moreover, the T1 and T2 quantifications had precision <5%, despite the lower SNR of 0.55 T.ConclusionA 3D whole-brain stack-of-spirals FISP MRF sequence is feasible for T1 and T2 mapping at 0.55 T.     

Wavelet domain de-noising of time-courses in MR image sequences

Magnetic resonance images acquired with high temporal resolution often exhibit large noise artifacts, which arise from physiological sources as well as from the acquisition hardware. These artifacts can be detrimental to the quality and interpretation of the time-course data in functional MRI studies. A class of wavelet-domain de-noising algorithms estimates the underlying, noise-free signal by thresholding (or 'shrinking') the wavelet coefficients, assuming the underlying temporal noise of each pixel is uncorrelated and Gaussian. A Wiener-type shrinkage algorithm is developed in this paper, for de-noising either complex- or magnitude-valued image data sequences. Using the de-correlation properties of the wavelet transform, as elucidated by Johnstone and Silverman, the assumption of i.i.d. Gaussian noise can be abandoned, opening up the possibility of removing colored noise. Both wavelet- and wavelet-packet based algorithms are developed, and the Wiener method is compared to the traditional Hard and Soft wavelet thresholding methods of Donoho and Johnstone. The methods are applied to two types of data sets. In the first, an artificial set of complex-valued images was constructed, in which each pixel has a simulated bimodal time-course. Gaussian noise was added to each of the real and imaginary channels, and the noise removed from the complex image sequence as well as the magnitude image sequence (where the noise is Rician). The bias and variance between the original and restored paradigms was estimated for each method. It was found that the Wiener method gives better balance in bias and variance than either Hard or Soft methods. Furthermore, de-noising magnitude data provides comparable accuracy of the restored images to that obtained from de-noising complex data. In the second data set, an actual in vivo complex image sequence containing unknown physiological and instrumental noise was used. The same bimodal paradigm as in the first data set was added to pixels in a small localized region of interest. For the paradigm investigated here, the smooth Daubechies wavelets provide better de-noising characteristics than the discontinuous Haar wavelets. Also, it was found that wavelet packet de-noising offers no significant improvement over the computationally more efficient wavelet de-noising methods. For the in vivo data, it is desirable that the groups of "activated" time-courses are homogeneous. It was found that the internal homogeneity of the group of time-courses increases when de-noising is applied. This suggests using de-noising as a pre-processing tool for both exploratory and inferential data analysis methods in fMRI.     

Flow properties of fast three-dimensional sequences for MR angiography

To reduce the scan time of time of flight or phase contrast angiography sequences, fast three-dimensional k-space trajectories can be employed. The best 3D trajectory depends on tolerable scan time, readout time, geometric flexibility, flow/motion properties and others. A formalism for flow/motion sensitivity comparison based on the velocity k-space behavior is presented. It consists in finding the velocity k-space position as a function of the spatial k-space position. The trajectories are compared graphically by their velocity k-space maps, with simulations and with an objective computed index. The flow/motion properties of various 3D trajectories (cones, spiral-pr hybrid, spherical stack of spirals, 3DFT, 3D echo-planar, and shells) were determined. In terms of flow/motion sensitivity the cones trajectory is the best, however, it is difficult to use it for anisotropic resolutions or fields of view. Tolerating more flow sensitivity, the stack of spirals trajectory offers more geometric flexibility.     

MR imaging with phase encoding of intermolecular multiple quantum coherences

Novel 2D and 3D pulse sequences producing images through the phase encoding of intermolecular multiple quantum coherences (i-MQCs) are presented. The signal acquired with these sequences is free from intermolecular zero quantum coherences (i-ZQCs) which are not phase encoded and additional phase cycling eliminates artifacts. Phase encoding during the n-quantum evolution period provides n times the resolution expected from equivalent phase encoding of the reconverted single quantum coherences. These sequences have potential applications for producing i-MQC images of biological tissues as well as nonbiological materials with substantial amounts of water.     

Spiral MR fingerprinting at 7 T with simultaneous B1 estimation

Magnetic resonance fingerprinting is an efficient, new approach for quantitative imaging with MR. We aimed to extend this technique to cases with B1 + inhomogeneities within the imaging volume.Previous approaches have used abrupt changes in flip angles to estimate the B1 + field simultaneously with T1 and T2, using a Cartesian approach in a small-animal scanner at 4.7 T. Here, we evaluated whether a similar approach would be suitable for imaging human brains using spiral readouts with a 7 T scanner.We found that our modified scheme could significantly reduce the adverse effects of B1 + inhomogeneities even in extreme cases, reducing both the bias and the variance in T2 estimations by an order of magnitude when compared to literature methods. Acquisitions used less than 1.5 W/kg SAR and could be performed in 12 s per slice.In conclusion, our approach can be used to perform quantitative imaging of the brain at 7 T in a short time, simultaneously estimating the B1 + profile.     

Spatial encoding and the single-scan acquisition of high definition MR images in inhomogeneous fields

We have recently proposed a protocol for retrieving multidimensional magnetic resonance spectra and images within a single scan, based on a spatial encoding of the spin interactions. The spatial selectivity of this encoding process also opens up new possibilities for compensating magnetic field inhomogeneities; not by demanding extreme uniformities from the B(0) fields, but by compensating for their effects at an excitation and/or refocusing level. This potential is hereby discussed and demonstrated in connection with the single-scan acquisition of high-definition multidimensional images. It is shown that in combination with time-dependent gradient and radiofrequency manipulations, the new compensation approach can be used to counteract substantial field inhomogenities at either global or local levels over relatively long periods of time. The new compensation scheme could find uses in areas where heterogeneities in magnetic fields present serious obstacles, including rapid studies in regions near tissue/air interfaces. The principles of the B(0) compensation method are reviewed for one- and higher-dimensional cases, and experimentally demonstrated on a series of 1D and 2D single-scan MRI experiments on simple phantoms.     

Improvement of image quality using BLADE sequences in brain MR imaging

The purpose of this study is to compare two types of sequences in brain magnetic resonance (MR) examinations of uncooperative and cooperative patients. For each group of patients, the pairs of sequences that were compared were two T2-weighted (T2-W) fluid attenuated inversion recovery sequences with different k-space trajectories (conventional Cartesian and BLADE) and two T2-TSE weighted with different k-space trajectories (conventional Cartesian and BLADE). Twenty-three consecutive uncooperative patients and 44 cooperative patients, who routinely underwent brain MR imaging examination, participated in the study. Both qualitative and quantitative analyses were performed based on the signal-to-noise ratio, contrast-to-noise ratio (CNR), and relative contrast (ReCon) measures of normal anatomic structures. The qualitative analysis was performed by experienced radiologists. Also, the presence of motion, other (e.g., Gibbs, susceptibility artifacts, phase encoding from vessels) artifacts and pulsatile flow artifacts was evaluated.     

Hadamard encoding with surface coils for high SNR MR spectroscopy.

The advantages of Hadamard over phase encoding in magnetic resonance spectroscopy (MRS) applied with surface coils in the direction perpendicular to the coil are demonstrated experimentally. With the recently introduced, time-shifted adiabatic pulses, the application of Hadamard encoding with surface coils results with almost ideal point spread function for pixels up to a distance of a radius from the coil. Comparison to phase encoding with equal region of interest size shows the significant advantage of Hadamard encoding in slice sharpness, overlapping, and spatial contamination. In addition, since there is no aliasing in Hadamard space, the total experimental time for the same region of interest is much shorter. We conclude that the hybrid of Hadamard encoding in the direction perpendicular to the coil and phase encoding in other directions is the method of choice to obtain reliable high signal to noise ratio MRS in vivo.     

Effects of RF pulse profile and intra-voxel phase dispersion on MR fingerprinting with balanced SSFP readout

PurposeTo investigate possible errors in T1 and T2 quantification via MR fingerprinting with balanced steady-state free precession readout in the presence of intra-voxel phase dispersion and RF pulse profile imperfections, using computer simulations based on Bloch equations.Materials and methodsA pulse sequence with TR changing in a Perlin noise pattern and a nearly sinusoidal pattern of flip angle following an initial 180-degree inversion pulse was employed. Gaussian distributions of off-resonance frequency were assumed for intra-voxel phase dispersion effects. Slice profiles of sinc-shaped RF pulses were computed to investigate flip angle profile influences. Following identification of the best fit between the acquisition signals and those established in the dictionary based on known parameters, estimation errors were reported. In vivo experiments were performed at 3 T to examine the results.ResultsSlight intra-voxel phase dispersion with standard deviations from 1 to 3 Hz resulted in prominent T2 under-estimations, particularly at large T2 values. T1 and off-resonance frequencies were relatively unaffected. Slice profile imperfections led to under-estimations of T1, which became greater as regional off-resonance frequencies increased, but could be corrected by including slice profile effects in the dictionary. Results from brain imaging experiments in vivo agreed with the simulation results qualitatively.ConclusionMR fingerprinting using balanced SSFP readout in the presence of intra-voxel phase dispersion and imperfect slice profile leads to inaccuracies in quantitative estimations of the relaxation times.     

Elimination of motion and pulsation artifacts using BLADE sequences in knee MR imaging

The purpose of this study is to evaluate the ability of proton density (PD)-BLADE sequences in reducing or even eliminating motion and pulsatile flow artifacts in knee magnetic resonance imaging examinations. Eighty consecutive patients, who had been routinely scanned for knee examination, participated in the study. The following pairs of sequences with and without BLADE were compared: (a) PD turbo spin echo (TSE) sagittal (SAG) fat saturation (FS) in 35 patients, (b) PD TSE coronal (COR) FS in 19 patients, (c) T2 TSE axial in 13 patients and (d) PD TSE SAG in 13 patients. Both qualitative and quantitative analyses were performed based on the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures of normal anatomic structures. The qualitative analysis was performed by experienced radiologists. Also, the presence of image motion and pulsation artifacts was evaluated. Based on the results of the SNR, CRN and ReCon for the different sequences and anatomical structures, the BLADE sequences were significantly superior in 19 cases, whereas the corresponding conventional sequences were significantly superior in only 6 cases. BLADE sequences eliminated motion artifacts in all the cases. However, motion artifacts were shown in (a) six PD TSE SAG FS, (b) three PD TSE COR FS, (c) three PD TSE SAG and (d) two T2 TSE axial conventional sequences. In our results, it was found that, in PD FS sequences (sagittal and coronal), the differences between the BLADE and conventional sequences regarding the elimination of motion and pulsatile flow artifacts were statistically significant. In all the comparisons, the PD FS BLADE sequences (coronal and sagittal) were significantly superior to the corresponding conventional sequences regarding the classification of their image quality. In conclusion, this technique appears to be capable to potentially eliminate motion and pulsatile flow artifacts in MR images.     

MR pulse sequences for selective relaxation time measurements: a phantom study

The accuracy of relaxation time measurements of spectroscopic inversion recovery and CPMG multi-echo pulse sequences together with ISIS and stimulated echo-pulse methods have been tested on a reference phantom (test object no. 5, of the EEC Concerted Research Project). For the measurements a Siemens Magnetom wholebody magnetic resonance scanner operating at 1.5 Tesla was used. For comparison six imaging pulse sequences for relaxation time measurements were tested on the same phantom. The spectroscopic pulse sequences all had an accuracy better than 10% of the reference values.     

Three-dimensional phase contrast MR cerebral venography with zero filling interpolation in the slice encoding direction.

The purpose of this study was to evaluate the magnetic resonance (MR) cerebral venography findings of a three-dimensional phase contrast MR sequence with zero filling interpolation of the data in the slice encoding direction. Fifty volunteers were enrolled in the study. Images were obtained on a 1.5 MR imaging system with acquisition time of 12 min. MIP images were reconstructed throughout the entire imaging volume. A grading scale system was used to assess dural venous sinuses, major deep veins, cortical, and cortical eponymic veins. Inferior group of dural venous sinuses, inferior sagittal sinus, and cortical eponymic veins were poorly demonstrated. Score of the superior sagittal sinus, the straight sinus, the confluence of the superior sinus group, the right transverse and sigmoid sinuses, the internal veins, and the vein of Galen was excellent. The score of the left transverse and sigmoid sinuses was good. In conclusion, when using zero filling interpolation of the data in a three-dimensional phase contrast MR cerebral venography sequence, the superior group of dural venous sinuses and main major deep veins are demonstrated with good conspicuity.     

Auxiliary phase encoding in multi spin-echo sequences: application to rapid current density imaging

Multi spin-echo sequences such as single-shot RARE are very sensitive to the initial phase of the transverse magnetization, and they can preserve only the transverse magnetization component which is aligned with the axis of the refocusing pulse rotation. Therefore, two separate single-shot RARE experiments with phases of refocusing pulses 90 degrees apart have to be run and their complex images summed to obtain an error-free phase map of the initial transverse magnetization. This is particularly useful when auxiliary phase encoding is integrated in the preparation period of the RARE sequence, such as when encoding flow, displacement, susceptibility, pH or temperature. In this paper, the two-shot RARE approach is verified first theoretically and then experimentally by demonstrating its application to rapid current density imaging (CDI). The sequence consists of the preparation period which triggers electric pulses in the sample followed by the RARE acquisition period. Electric currents through the sample induce a magnetic field change in the direction of the static magnetic field and a phase change of the initial magnetization proportional to it. To calculate one component of current density two orthogonal components of magnetic field change must be measured. In general, for 2D non-symmetrical samples, this can be done by rotating the sample to a perpendicular orientation. The proposed CDI method allows much for faster magnetic field change mapping than the standard spin-echo based CDI.     

Hybrid WDMA/OCDM system with the capability of encoding multiple wavelength channels by employing one encoder and one corresponding optical code

<正>A hybrid wavelength division multiple access(WDMA)/optical code division multiplexing(OCDM) system is proposed,where the optical code is not the same as the address of every optical network unit(ONU); rather,the code is a virtual fiber of hybrid passive optical network(PON).To our knowledge,this is the first report analyzing a single encoder/decoder with a single corresponding optical code being exploited to encode/decode multiple wavelength signals simultaneously.This system enables OCDM to become transparent to ONU so that the existing wavelength division multiplexing(WDM) PON can be upgraded. Thus,redesigning the optical line terminal and ONU can be easily accomplished,and greatly decreasing the number of encoder/decoder becomes possible.In experiment,we only employ two encoder/decoder pairs to combine two WDM-PONs in one fiber.Simulation results confirm the feasibility of the proposed system.     

MR Imaging of total hip arthroplasty: comparison among sequences to study the sciatic nerve at 1.5 T

Purpose

This study was done to test a series of MR sequences for evaluating the sciatic nerve after total hip arthroplasty (THA).

Material and Methods

The study protocol was approved by the institutional review board. Informed consent was obtained from all patients. Twenty-five patients (11 men and 14 women mean age: 62.3±5.7 years) with THA were included in this prospective study. MRI protocol included sequences that were preliminarily tailored for nerve imaging in patients with THA: proton density (PD)-weighted turbo SE, T1-weighted turbo SE (TSE) 3 mm thickness, T1-weighted turbo SE (TSE) 6 mm thickness, T1-weighted turbo SE with high bandwidth (TSE hBW), T2- weighted TSE, T2-weighted with fat saturation and short-tau inversion recovery (STIR). For each sequence, we evaluated the visibility of the sciatic nerve using a semiquantitative score (0=total masking; 1=insufficient visibility; 2=sufficient visibility; 3=optimal visibility). The sum of the scores given to each sequence was divided by the maximal sum, obtaining a percentage visibility index. Friedman and sign tests were used for statistical analysis.

Results

MR examination time was approximately 40 min. No patients reported pain, heat or symptoms related to nerve stimulation. The visibility index ranged between 88% and 70% for the first four sequences. The T1-weighted TSE hBW sequence had the best visibility index (P<.05). The visibility indexes of the first four sequences were significantly higher (P<.004, sign test) than those of the remaining three sequences.

Conclusion

The sciatic nerve could be studied at 1.5 T in patients following THA. The nerve is better visualized with T1-weighted TSE hBW sequences. On T2-weighted sequences and STIR, the visibility of the nerve is low.     

A statistical method for predicting alpha-helical and beta-sheet regions in proteins from their amino acidic sequences

Summary In this paper we propose a new method to predict the secondary structure of proteins from sequence data. A satisfactory improvement of the available efficiency of prediction is obtained. The described method takes into account the frequency of each pair of amino acids in alpha-helical, beta-sheet and random coil regions according to previous results that the sequences of amino acidic residues in these regions are autocorrelated. The rules of the method are not derived from the analysis of the regions of proteins with a known secondary structure, but they are instead based on statistical considerations. In such a way the obtained value of efficiency of the method (88%) has a high reliability: in fact, it is correct to test a method only on the data not used to construct it. A new definition of efficiency of a predictive method is given to resolve the ambiguities arising from the previously accepted definitions.

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Riassunto In questo lavoro si propone un nuovo algoritmo per predire la struttura secondaria di una proteina dall’analisi della sua sequenza aminoacidica, con il quale si è ottenuto un significativo miglioramento delle efficienze di previsione della struttura secondaria disponibili fino ad ora. Il metodo descritto tiene conto della frequenza delle coppie adiacenti di aminoacidi nelle regioni ad alpha-helix, beta sheet e random coil, in accordo con il nostro precedente risultato che in tali regioni le sequenze aminoacidiche sono autocorrelate. Le regole usate non derivano dall’analisi delle regioni di proteine con una struttura secondaria nota, ma sono invece basate esclusivamente su considerazioni statistiche. In tal modo il valore ottenuto per l’efficienza del metodo (88%) ha un’alta affidabilità, essendo corretto controllare un metodo solo sui dati non utilizzati per la sua costruzione. Per risolvere le ambiguità esistenti, inoltre, si dà qui una nuova definizione di efficienza per un metodo di previsione di strutture secondarie.

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Резюме В этой работе предлагается новый метод для предсказания вторичной структуры белков, исходя из последовательности аминокислот. Получается существенное улучшение эффективности предсказания. Предложенный метод учитывает частоту каждой пары аминокислот в альфа-спиральной области, бета-слоистой области и в области случайных спиралей, в соответствии с предыдущими результатами, согласно которым последовательности аминокислот в этих областях являются автокоррелированными. Правила метода не выводятся из анализа областей белков с известной вторичной структурой, а основываются на статистических рассмотрениях. Полученное значение эффективности (88%) имеет высокую надежность. Корректность метода проверялась не только на данных, использованных для его конструирования. Предлагается новое определение эффективности для разрешения неоднозначностей, связанных с ранее принятыми определениями.