Comparison ofMultiecho Postprocessing Schemes for SWI with Use of Linear and NonlinearMask Functions

BACKGROUND AND PURPOSE: SWI is an MR technique conventionally implemented with single-echo gradient-echo data. The purpose of this study was to compare single-echo SWI processing and 2 multiecho SWI processing schemes: postaverage, where an SWI image is created for each echo and then averaged to create a single volume; and frequency-based, where a SWI image is generated from an average frequency image. Linear and nonlinear mask functions were investigated for all 3 processing schemes. MATERIALS ANDMETHODS: Comprehensive optimizations were performed. Single and multigradient-echo data were acquired at 3T in 10 volunteers. Contrast-to-noise ratio was measured in various structures. Visibilities of the same structures were ranked in different SWI images by trained raters. RESULTS: When image evaluation was based on measurements of contrast-to-noise ratio, the nonlinear mask and frequency-based scheme were superior. However, when image evaluation was based on ranks of qualitative visibility, the linear mask and postaverage scheme were superior. Although the nonlinear mask and frequency-based scheme allow increased contrast of paramagnetic perturbers such as the globus pallidus, periventricular veins, red nucleus, and subthalamic nucleus, they do not necessarily increase the information content of the image; rather, they result in a harsh contrast that is visually unpleasing to radiologists and wherein more subtle structure is relatively less apparent. CONCLUSIONS: Linearly masked postaverage SWI is the recommended implementation of multiecho SWI for radiologic use; however, nonlinearly masked frequency-based SWI may have use in computer-based segmentation or registration. ABBREVIATIONS: CNR contrast-to-noise ratio; GP globus pallidus; OR optic radiations; RN red nucleus; STN subthalamic nucleus SWI is an MR imaging technique that exploits the effect of variations in magnetic susceptibility on gradient-echo signal to produce enhanced image contrast. Most MR imaging studies reconstruct only the magnitude image; phase is generally discarded. However, the phase data contain potentially useful information about inclusions in the imaging volume that change the local magnetic field. SWI processing allows this information to be incorporated into the magnitude image because the underlying structure may not necessarily be visible on magnitude alone. SWI was originally used to produce high-resolution venograms. SWI has found additional uses in clinical and research settings because of its sensitivity to other physiologically relevant magnetic field perturbers such as blood products, iron, and calcium. However, single-echo SWI is useful in the visualization, but not the quantification, of field perturbers. Modifications of SWI allow simultaneous quantification of the nature or amount of the perturber. For example, the effective transverse relaxation rate (R2 ), which can be extracted from multiecho gradient-echo data via voxelwise curve fitting, is a metric that scales linearly with iron concentration in the brain. Brainovich et al described a postprocessing scheme for dualecho gradient-echo data. In this scheme, average phase and average magnitude volumes were generated and subsequently used to produce a single SWI volume. Denk and Rauscher used a multiecho acquisition with 5 echoes to produce 5 SWI volumes that Received December 13, 2012; accepted after revision February 14, 2013. From the Departments of Medical Biophysics (M.P.Q., R.S.M.) and Medical Imaging (A.W.L., J.R.B., S.E.L.), Western University, London, Ontario, Canada; and Robarts Research Institute (M.P.Q., J.S.G., L.M.K., R.S.M.), London, Ontario, Canada. This work was supported in part by grants from the Canadian Institutes of Health Research (MOP-111085) and Canada Research Chairs Program (R.S.M.), and from the Vanier Canada Graduate Scholarships Program (M.P.Q). Paper previously presented at: Annual Meeting of International Society for Magnetic Resonance in Medicine, May 10, 2012; Melbourne, Australia. Please address correspondence to Matthew P. Quinn, Centre for Functional and Metabolic Mapping, Robarts Research Institute, 100 Perth Dr, London, Ontario, Canada, N6A5K8; e-mail: mquinn@robarts.ca Indicates open access to non-subscribers at www.ajnr. org Indicates article with supplemental on-line figures http://dx.doi. org/10.3174/ajnr.A3584 AJNR Am J Neuroradiol ●:● ● 2013 www.ajnr. org 1 Published June 6, 2013 as 10.3174/ajnr.A3584 Copyright 2013 by American Society of Neuroradiology. were subsequently averaged to produce a single average SWI volume. They reported improvements in contrast-to-noise ratio (CNR) of veins compared with conventional SWI. In addition, they described computation of R2 maps as a natural extension of the multiecho acquisition. In all cases, a conventional linearphase mask function for SWI was used. The use of alternative mask functions theoretically results in an increased CNR of the cerebral veins, though this claim has not been rigorously tested in vivo. There are 2 main goals of this work: first, a comparison of 3 SWI postprocessing schemes (single echo and 2 multiecho methods); and second, a comparison of the conventional (ie, linear) mask function with a novel nonlinear mask function. We identified the following objectives: 1) to describe and outline modifications to previously published multiecho SWI, as well as describe a nonlinear mask function; 2) to optimize the number of mask function multiplications for all combinations of postprocessing scheme and mask function; and 3) to compare all postprocessing schemes and mask functions in vivo by using both quantitative and radiologic assessments. MATERIALS AND METHODS Processing was performed in Matlab (MathWorks, Natick, Massachusetts) and FSL (http://www.fmrib.ox.ac.uk/fsl). Statistical analyses were performed in SPSS (IBM, Armonk, New York). SWI Postprocessing Schemes Three postprocessing schemes were compared: 1 for single-echo SWI and 2 for multiecho SWI. First, single-echo SWI processing involves background phase removal by using the homodyne method, generation of a phase mask, and multiplication of the m power of the mask by the magnitude image. Second, the multiecho SWI method of Denk and Rauscher was modified and herein is referred to as the postaverage method. Postaverage multiecho SWI involves single-echo SWI processing on data from each echo, and averaging of the resulting images. Denk and Rauscher prescribe this technique with a linearly (in TE) increasing homodyne filter width to remove background contributions to phase from each echo to account for the additional phase wrapping at longer TE. We used a constant (with TE) filter size, as a compromise between eliminating phase wraps in later echoes and preserving the relevant contrast between echoes in a consistent manner. Third, a frequency-based method for multiecho SWI was used and is based on the method described initially by Brainovich et al. For the image volume reconstructed from each echo, the background phase was removed by use of the homodyne method. Successive phase images were then temporally unwrapped by using Matlab’s 1D unwrap function on the TE-dependent voxel data. Each unwrapped phase image was then divided by its corresponding TE to produce a frequency image. A weighted average of frequency was calculated from these individual frequency images: weights were inversely proportional to the variance of the frequency: (magnitude) (TE). A mask was computed from the average frequency image, and its m power was multiplied by the average magnitude image for that section. This method is similar to what has been described by Brainovich et al but, in addition, involves the temporal unwrapping of phase, as well as masking the weighted average of frequency maps rather than the arithmetic mean of the phase images. Although the mean of the frequency maps is a physical and intuitive quantity, the mean of the phase images used by Brainovich et al is not logical from a physical or mathematic perspective. For the homodyne filter, a 2D Hann window (1 period of a raised cosine) with dimensions equal to 30% (for multiecho) or 20% (for single-echo) of the respective matrix dimensions, rounded to the nearest integer, was used. This constant width filter, in conjunction with the temporal phase unwrapping that was used, resulted in the ability to remove all relevant phase wraps. SWI Mask Functions Two different mask functions were compared. First, the conventional linear mask function was used. In general form, the linear mask, L, is defined as follows: