Inter-site and inter-scanner diffusion MRI data harmonization.

We propose a novel method to harmonize diffusion MRI data acquired from multiple sites and scanners, which is imperative for joint analysis of the data to significantly increase sample size and statistical power of neuroimaging studies. Our method incorporates the following main novelties: i) we take into account the scanner-dependent spatial variability of the diffusion signal in different parts of the brain; ii) our method is independent of compartmental modeling of diffusion (e.g., tensor, and intra/extra cellular compartments) and the acquired signal itself is corrected for scanner related differences; and iii) inter-subject variability as measured by the coefficient of variation is maintained at each site. We represent the signal in a basis of spherical harmonics and compute several rotation invariant spherical harmonic features to estimate a region and tissue specific linear mapping between the signal from different sites (and scanners). We validate our method on diffusion data acquired from seven different sites (including two GE, three Philips, and two Siemens scanners) on a group of age-matched healthy subjects. Since the extracted rotation invariant spherical harmonic features depend on the accuracy of the brain parcellation provided by Freesurfer, we propose a feature based refinement of the original parcellation such that it better characterizes the anatomy and provides robust linear mappings to harmonize the dMRI data. We demonstrate the efficacy of our method by statistically comparing diffusion measures such as fractional anisotropy, mean diffusivity and generalized fractional anisotropy across multiple sites before and after data harmonization. We also show results using tract-based spatial statistics before and after harmonization for independent validation of the proposed methodology. Our experimental results demonstrate that, for nearly identical acquisition protocol across sites, scanner-specific differences can be accurately removed using the proposed method.

A new quantitative evaluation method for age-related changes of individual pigmented spots in facial skin.

BACKGROUND: Facial skin pigmentation is one of the most prominent visible features of skin aging and often affects perception of health and beauty. To date, facial pigmentation has been evaluated using various image analysis methods developed for the cosmetic and esthetic fields. However, existing methods cannot provide precise information on pigmented spots, such as variations in size, color shade, and distribution pattern. The purpose of this study is the development of image evaluation methods to analyze individual pigmented spots and acquire detailed information on their age-related changes. METHODS: To characterize the individual pigmented spots within a cheek image, we established a simple object-counting algorithm. First, we captured cheek images using an original imaging system equipped with an illumination unit and a high-resolution digital camera. The acquired images were converted into melanin concentration images using compensation formulae. Next, the melanin images were converted into binary images. The binary images were then subjected to noise reduction. Finally, we calculated parameters such as the melanin concentration, quantity, and size of individual pigmented spots using a connected-components labeling algorithm, which assigns a unique label to each separate group of connected pixels. RESULTS: The cheek image analysis was evaluated on 643 female Japanese subjects. We confirmed that the proposed method was sufficiently sensitive to measure the melanin concentration, and the numbers and sizes of individual pigmented spots through manual evaluation of the cheek images. The image analysis results for the 643 Japanese women indicated clear relationships between age and the changes in the pigmented spots. CONCLUSION: We developed a new quantitative evaluation method for individual pigmented spots in facial skin. This method facilitates the analysis of the characteristics of various pigmented facial spots and is directly applicable to the fields of dermatology, pharmacology, and esthetic cosmetology.

Validating a new methodology for optical probe design and image registration in fNIRS studies.

Functional near-infrared spectroscopy (fNIRS) is an imaging technique that relies on the principle of shining near-infrared light through tissue to detect changes in hemodynamic activation. An important methodological issue encountered is the creation of optimized probe geometry for fNIRS recordings. Here, across three experiments, we describe and validate a processing pipeline designed to create an optimized, yet scalable probe geometry based on selected regions of interest (ROIs) from the functional magnetic resonance imaging (fMRI) literature. In experiment 1, we created a probe geometry optimized to record changes in activation from target ROIs important for visual working memory. Positions of the sources and detectors of the probe geometry on an adult head were digitized using a motion sensor and projected onto a generic adult atlas and a segmented head obtained from the subject's MRI scan. In experiment 2, the same probe geometry was scaled down to fit a child's head and later digitized and projected onto the generic adult atlas and a segmented volume obtained from the child's MRI scan. Using visualization tools and by quantifying the amount of intersection between target ROIs and channels, we show that out of 21 ROIs, 17 and 19 ROIs intersected with fNIRS channels from the adult and child probe geometries, respectively. Further, both the adult atlas and adult subject-specific MRI approaches yielded similar results and can be used interchangeably. However, results suggest that segmented heads obtained from MRI scans be used for registering children's data. Finally, in experiment 3, we further validated our processing pipeline by creating a different probe geometry designed to record from target ROIs involved in language and motor processing.

Effectiveness of a silicone device for foot MRI in order to obtain homogeneous fat suppression images.

BACKGROUND: Incomplete fat suppression induced by magnetic field inhomogeneity is difficult to compensate for with hardware magnetic-field shimming. PURPOSE: To evaluate the effectiveness of a silicone device used to obtain homogeneous fat suppression during 3T magnetic resonance imaging (MRI) scans of the foot. MATERIAL AND METHODS: Thirty-eight healthy volunteers were enrolled and examined twice, before (group A) and after (group B) the application of a silicone device. Fat-saturated, T2-weighted, fast spin-echo images were acquired using the same scanning protocol at both examinations. Signal- and contrast-to-noise ratios (SNR and CNR) were calculated and compared in the four regions of interest (ROIs). ROI 1 and 2 were selected from toe-side bone and soft tissue, while ROI 3 and 4 were selected from proximal bone and soft tissue. Qualitative analysis using a four-point scale was performed for three categories. The categories are as follows: the overall image quality, homogeneity of the first phalange and metatarsal bone, respectively. RESULTS: The SNR and CNR in ROI 1 and 2 were significantly higher in group A than in group B (SNR; P < 0.001, CNR; P < 0.001), and there were no significant difference in ROI 3 and 4. The qualitative score of the overall fat suppression in group B was significantly higher than that in group A (P < 0.001). Homogeneity of the first phalange in group B was also significantly higher than that in group A (P < 0.001). On the other hand, the homogeneity of the metatarsal bone was not significantly different in the two groups. CONCLUSION: The use of a silicone device provides homogeneous fat suppression in 3T MRI of the foot and can significantly improve image quality.

Towards acousto-optic tissue imaging with nanosecond laser pulses.

We present a way to generate acousto-optical signals in timovssue-like media with nanosecond laser pulses. Our method is based on recording and analyzing speckle patterns formed by interaction of nanosecond laser pulses with tissue, without and with simultaneous application of ultrasound. Stroboscopic application allows visualizing the temporal behavior of speckles while the ultrasound is propagating through the medium. We investigate two ways of quantifying the acousto-optic effect, viz. adding and subtracting speckle patterns obtained at various ultrasound phases. Both methods are compared with the existing speckle contrast method using a 2D scan and are found to perform similarly. Our method gives outlook on overcoming the speckle decorrelation problem in acousto-optics, and therefore brings in-vivo acousto-optic measurements one step closer. Furthermore it enables combining acousto-optics and photoacoustics in one setup with a single laser.

Trends in correlation-based pattern recognition and tracking in forward-looking infrared imagery.

In this paper, we review the recent trends and advancements on correlation-based pattern recognition and tracking in forward-looking infrared (FLIR) imagery. In particular, we discuss matched filter-based correlation techniques for target detection and tracking which are widely used for various real time applications. We analyze and present test results involving recently reported matched filters such as the maximum average correlation height (MACH) filter and its variants, and distance classifier correlation filter (DCCF) and its variants. Test results are presented for both single/multiple target detection and tracking using various real-life FLIR image sequences.

A subtractive radiographic template for computer-guided surgery.

The procedure for creating a computer-aided design/computer-aided manufactured surgical template with the NobelClinician software was originally designed for the completely edentulous arch. With the development of new techniques and expanded functions in the software, guided surgery for the partially edentulous became a viable option. As of yet, few protocols have been reported for the guided surgery of immediate implants with the NobelClinician software. A new technique is described whereby the radiographic template is modified to allow the use of guided surgery for the immediate placement of dental implants after extractions.

[Development of a digital chest phantom for studies on energy subtraction techniques].

Digital chest phantoms continue to play a significant role in optimizing imaging parameters for chest X-ray examinations. The purpose of this study was to develop a digital chest phantom for studies on energy subtraction techniques under ideal conditions without image noise. Computed tomography (CT) images from the LIDC (Lung Image Database Consortium) were employed to develop a digital chest phantom. The method consisted of the following four steps: 1) segmentation of the lung and bone regions on CT images; 2) creation of simulated nodules; 3) transformation to attenuation coefficient maps from the segmented images; and 4) projection from attenuation coefficient maps. To evaluate the usefulness of digital chest phantoms, we determined the contrast of the simulated nodules in projection images of the digital chest phantom using high and low X-ray energies, soft tissue images obtained by energy subtraction, and "gold standard" images of the soft tissues. Using our method, the lung and bone regions were segmented on the original CT images. The contrast of simulated nodules in soft tissue images obtained by energy subtraction closely matched that obtained using the gold standard images. We thus conclude that it is possible to carry out simulation studies based on energy subtraction techniques using the created digital chest phantoms. Our method is potentially useful for performing simulation studies for optimizing the imaging parameters in chest X-ray examinations.

Hybrid ultra-low-field MRI and magnetoencephalography system based on a commercial whole-head neuromagnetometer.

Ultra-low-field MRI uses microtesla fields for signal encoding and sensitive superconducting quantum interference devices for signal detection. Similarly, modern magnetoencephalography (MEG) systems use arrays comprising hundreds of superconducting quantum interference device channels to measure the magnetic field generated by neuronal activity. In this article, hybrid MEG-MRI instrumentation based on a commercial whole-head MEG device is described. The combination of ultra-low-field MRI and MEG in a single device is expected to significantly reduce coregistration errors between the two modalities, to simplify MEG analysis, and to improve MEG localization accuracy. The sensor solutions, MRI coils (including a superconducting polarizing coil), an optimized pulse sequence, and a reconstruction method suitable for hybrid MEG-MRI measurements are described. The performance of the device is demonstrated by presenting ultra-low-field-MR images and MEG recordings that are compared with data obtained with a 3T scanner and a commercial MEG device.

Monochromatic verification of high-contrast imaging with an occulter.

One of the most promising concepts of starlight suppression for direct imaging of exoplanets is flying a specially-shaped external occulter in formation with a space telescope. Here we present contrast performance verification of an occulter design scaled to laboratory-size using Fresnel numbers corresponding to the space design. Experimental design innovations include usage of an expanding beam to minimize phase aberrations, and an outer ring to minimize hard-edge diffraction effects. The apodizing performance of the optimized occulter edge is compared with a baseline case of a circular occulter and shown to result in contrast improvements. Experimental results in red monochromatic light show that the achieved laboratory contrast exceeds ten orders of magnitude, but with differences from the theoretical diffraction analysis limited by specular reflection from the mask edges.

Transport of intensity phase reconstruction to solve the twin image problem in holographic x-ray imaging.

We have implemented a deterministic method for solving the phase problem in hard x-ray in-line holography which overcomes the twin image problem. The phase distribution in the detector plane is retrieved by using two images with slightly different Fresnel numbers. We then use measured intensities and reconstructed phases in the detection plane to compute the exit wave in the sample plane. No further a priori information like a limited support or the assumption of pure phase objects is necessary so that it can be used for a wide range of complex samples. Using a nano-focused hard x-ray beam half period resolutions better than 30 nm are achieved.

Integrated optical- and acoustic-resolution photoacoustic microscopy based on an optical fiber bundle.

Photoacoustic microscopy (PAM), whose spatial resolution and maximum imaging depth are both scalable, has made great progress in recent years. However, each PAM system currently achieves only one resolution with an associated maximum imaging depth. Here, we present an integrated optical-resolution (OR) and acoustic-resolution (AR) PAM system implemented by delivering light via an optical fiber bundle. A single fiber core is used to deliver light for OR illumination in order to achieve a small spot size and hence high lateral resolution, whereas all the fiber cores are used to deliver more energy for AR illumination. Most other components are shared by the OR and AR imaging. The lateral resolution can be seamlessly switched between 2.2 and 40 µm as the maximum imaging depth is switched between 1.3 and 3.0 mm. The system enables automatically coregistered higher-resolution OR and deeper AR photoacoustic imaging.

Combined photoacoustic and optical coherence tomography using a single near-infrared supercontinuum laser source.

We developed an integrated dual-modal photoacoustic and optical coherence tomography (PA-OCT) system using a single near-infrared supercontinuum laser source to simultaneously provide both optical absorption and scattering contrasts. A pulsed broadband supercontinuum source was generated by a pulsed Nd:YAG laser and a photonic-crystal fiber. When we imaged two colored hairs, the black hair was visible in both PA and OCT images, whereas the white hair was only mapped in the OCT image. The single laser source will potentially allow us to implement relatively simple, cheap, and compact dual-modal PA-OCT systems, which are key criteria for fast clinical translation and commercialization.

Miniature probe combining optical-resolution photoacoustic microscopy and optical coherence tomography for in vivo microcirculation study.

Photoacoustic microscopy (PAM) is sensitive to optical absorption, while optical coherence tomography (OCT) is based on optical backscattering. Combining PAM and OCT can provide complementary information about biological tissue. Here we present a combined optical-resolution PAM (ORPAM) and OCT system that is integrated through a miniature probe with an overall diameter of 2.3 mm, suitable for insertion through a standard endoscopic or laparoscopic port during minimally invasive surgery or endoscopic exam. The hybrid probe consists of a common optical path for OCT (light delivery/detection) and ORPAM (light excitation) and a 10 MHz unfocused ultrasound transducer for photoacoustic detection. The combined system yields a lateral resolution of 15 µm for both ORPAM and OCT.

A parallel imaging approach to wide-field MR microscopy.

Magnetic resonance microscopy, suggested in the earliest papers on MRI, has always been limited by the low signal-to-noise ratio resulting from the small voxel size. Magnetic resonance microscopy has largely been enabled by the use of microcoils that provide the signal-to-noise ratio improvement required to overcome this limitation. Concomitant with the small coils is a small field-of-view, which limits the use of magnetic resonance microscopy as a histological tool or for imaging large regions in general. This article describes initial results in wide field-of-view magnetic resonance microscopy using a large array of narrow, parallel coils, which provides a signal-to-noise ratio enhancement as well as the ability to use parallel imaging techniques. Comparison images made between a volume coil and the proposed technique demonstrate reductions in imaging time of more than 100 with no loss in signal-to-noise ratio or resolution.

Dynamic light scattering optical coherence tomography.

We introduce an integration of dynamic light scattering (DLS) and optical coherence tomography (OCT) for high-resolution 3D imaging of heterogeneous diffusion and flow. DLS analyzes fluctuations in light scattered by particles to measure diffusion or flow of the particles, and OCT uses coherence gating to collect light only scattered from a small volume for high-resolution structural imaging. Therefore, the integration of DLS and OCT enables high-resolution 3D imaging of diffusion and flow. We derived a theory under the assumption that static and moving particles are mixed within the OCT resolution volume and the moving particles can exhibit either diffusive or translational motion. Based on this theory, we developed a fitting algorithm to estimate dynamic parameters including the axial and transverse velocities and the diffusion coefficient. We validated DLS-OCT measurements of diffusion and flow through numerical simulations and phantom experiments. As an example application, we performed DLS-OCT imaging of the living animal brain, resulting in 3D maps of the absolute and axial velocities, the diffusion coefficient, and the coefficient of determination.

A digital x-ray tomosynthesis coupled near infrared spectral tomography system for dual-modality breast imaging.

A Near Infrared Spectral Tomography (NIRST) system has been developed and integrated into a commercial Digital Breast Tomosynthesis (DBT) scanner to allow structural and functional imaging of breast in vivo. The NIRST instrument uses an 8-wavelength continuous wave (CW) laser-based scanning source assembly and a 75-element silicon photodiode solid-state detector panel to produce dense spectral and spatial projection data from which spectrally constrained 3D tomographic images of tissue chromophores are produced. Integration of the optical imaging system into the DBT scanner allows direct co-registration of the optical and DBT images, while also facilitating the synergistic use of x-ray contrast as anatomical priors in optical image reconstruction. Currently, the total scan time for a combined NIRST-DBT exam is ~50s with data collection from 8 wavelengths in the optical scan requiring ~42s to complete. The system was tested in breast simulating phantoms constructed using intralipid and blood in an agarose matrix with a 3 cm x 2 cm cylindrical inclusion at 1 cm depth from the surface. Diffuse image reconstruction of total hemoglobin (HbT) concentration resulted in accurate recovery of the lateral size and position of the inclusion to within 6% and 8%, respectively. Use of DBT structural priors in the NIRST reconstruction process improved the quantitative accuracy of the HbT recovery, and led to linear changes in imaged versus actual contrast, underscoring the advantages of dual-modality optical imaging approaches. The quantitative accuracy of the system can be further improved with independent measurements of scattering properties through integration of frequency or time domain data.

Methods for registration of magnetic resonance images of ex vivo prostate specimens with histology.

PURPOSE: To evaluate two methods of scanning and tissue processing to achieve accurate magnetic resonance (MR)-histologic correlation in human prostate specimens. MATERIALS AND METHODS: Two prostates had acrylic paint markers injected to define the plane of imaging and serve as internal fiducials. Each was placed on a polycarbonate plane-finder device (PFD), which was adjusted to align the imaging and cutting planes. Three prostates were aligned by use of a plane finder key (PFK), a polycarbonate plate that locks the specimen in a cylindrical carrier. Markers were injected for registration analysis. Prostates were imaged, then sectioned. Imaging software was used to create registration maps of the MR and histology images. Measurements between control points were made and compared. RESULTS: Accurate correlation was achieved between MR and histologic images. The mean displacement (MD) between the corresponding registration points using the PFD technique ranged from 1.11-1.38 mm for each section. The MD for all sections was 1.24 mm. The MD using the PFK technique ranged from 0.79-1.01 mm for each section, and the MD across all sections for the PFK was 0.92 mm. CONCLUSION: We describe two methods that can achieve accurate, reproducible correlation between MR imaging and histologic sections in human prostatectomy specimens.

An anthropomorphic polyvinyl alcohol brain phantom based on Colin27 for use in multimodal imaging.

PURPOSE: In this paper, the method for the creation of an anatomically and mechanically realistic brain phantom from polyvinyl alcohol cryogel (PVA-C) is proposed for validation of image processing methods such as segmentation, reconstruction, registration, and denoising. PVA-C is material widely used in medical imaging phantoms because of its mechanical similarities to soft tissues. METHODS: The phantom was cast in a mold designed using the left hemisphere of the Colin27 brain dataset [C. Holmes et al., "Enhancement of MR images using registration for signal averaging," J. Comput. Assist. Tomogr. 22(2), 324 (1998)]. Marker spheres and inflatable catheters were also implanted to enable good registration comparisons and to simulate tissue deformation, respectively. RESULTS: The phantom contained deep sulci, a complete insular region, and an anatomically accurate left ventricle. It was found to provide good contrast in triple modality imaging, consisting of computed tomography, ultrasound, and magnetic resonance imaging. Multiple sets of multimodal data were acquired from this phantom. CONCLUSIONS: The methods for building the anatomically accurate, multimodality phantom were described in this work. All multimodal data are made available freely to the image processing community (http://pvabrain.inria.fr). We believe the phantom images could allow for the validation and further aid in the development of novel medical image processing techniques.

A realistic deformable prostate phantom for multimodal imaging and needle-insertion procedures.

PURPOSE: Phantoms are a vital step for the preliminary validation of new image-guided procedures. In this paper, the authors present a deformable prostate phantom for use with multimodal imaging (end-fire or side-fire ultrasound, CT and MRI) and more specifically for transperineal or transrectal needle-insertion procedures. It is made of soft polyvinyl chloride (PVC) plastic and includes a prostate, a perineum, a rectum, a soft periprostatic surrounding and embedded targets for image registration and needle-targeting. Its main particularity is its realistic deformability upon manipulation. METHODS: After a detailed manufacturing description, the imaging and mechanical characteristics of the phantom are described and evaluated. First, the speed of sound and stress-strain relationship of the PVC material used in the phantom are described, followed by an analysis of its storage, imaging, needle-insertion force, and deformability characteristics. RESULTS: The average speed of sound in the phantom was measured to be 1380 ± 20 m/s, while the stress-strain relationship was found to be viscoelastic and in the range of typical prostatic tissues. The mechanical and imaging characteristics of the phantom were found to remain stable at cooler storage temperatures. The phantom had clearly distinguishable morphology in all three imaging modalities, with embedded targets that could be precisely segmented, resulting in an average US-CT rigid registration error of 0.66 mm. The mobility of the phantom prostate upon needle insertion was between 2 and 4 mm, with rotations between 0° and 2°, about the US probe head. CONCLUSION: The phantom's characteristics compare favorably with in vitro and in vivo measurements found in the literature. The authors believe that this realistic phantom could be of use to researchers studying new needle-based prostate diagnosis and therapy techniques.