Segmentation and visualization of a large, high-resolution micro-CT data of mice.

High-resolution large datasets were acquired to improve the understanding of murine bone physiology. The purpose of this work is to present the challenges and solutions in segmenting and visualizing bone in such large datasets acquired using micro-CT scan of mice. The analyzed dataset is more than 50 GB in size with more than 6,000 2,048 × 2,048 slices. The study was performed to automatically measure the bone mineral density (BMD) of the entire skeleton. A global Renyi entropy (GREP) method was initially used for bone segmentation. This method consistently oversegmented skeletal region. A new method called adaptive local Renyi entropy (ALREP) is proposed to improve the segmentation results. To study the efficacy of the ALREP, manual segmentation was performed. Finally, a specialized high-end remote visualization system along with the software, VirtualGL, was used to perform remote rendering of this large dataset. It was determined that GREP overestimated the bone cross-section by around 30 % compared with ALREP. The manual segmentation process took 6,300 min for 6,300 slices while ALREP took only 150 min for segmentation. Automatic image processing with ALREP method may facilitate BMD measurement of the entire skeleton in a significantly reduced time, compared with manual process.

Cone-beam micro-CT system based on LabVIEW software.

Construction of a cone-beam computed tomography (CBCT) system for laboratory research usually requires integration of different software and hardware components. As a result, building and operating such a complex system require the expertise of researchers with significantly different backgrounds. Additionally, writing flexible code to control the hardware components of a CBCT system combined with designing a friendly graphical user interface (GUI) can be cumbersome and time consuming. An intuitive and flexible program structure, as well as the program GUI for CBCT acquisition, is presented in this note. The program was developed in National Instrument's Laboratory Virtual Instrumentation Engineering Workbench (LabVIEW) graphical language and is designed to control a custom-built CBCT system but has been also used in a standard angiographic suite. The hardware components are commercially available to researchers and are in general provided with software drivers which are LabVIEW compatible. The program structure was designed as a sequential chain. Each step in the chain takes care of one or two hardware commands at a time; the execution of the sequence can be modified according to the CBCT system design. We have scanned and reconstructed over 200 specimens using this interface and present three examples which cover different areas of interest encountered in laboratory research. The resulting 3D data are rendered using a commercial workstation. The program described in this paper is available for use or improvement by other researchers.

White matter measures correlate with essential tremor severity-A pilot diffusion tensor imaging study.

BACKGROUND: An evolving pathophysiological concept of essential tremor (ET) points to diffuse brain network involvement, which emphasizes the need to investigate white matter (WM) changes associated with motor symptoms of ET. OBJECTIVES: To investigate ET-related WM changes and WM correlates of tremor severity using tremor clinical rating scales and accelerometry. METHODS: Tract-based spatial statistics (TBSS) approach was utilized to compare 3 Tesla diffusion tensor imaging (DTI) data from 12 ET patients and 10 age- and gender-matched healthy individuals. Clinical scales, tremor frequency and amplitude as measured by accelerometry were correlated with DTI data. RESULTS: ET patients demonstrated mean (MD) and radial diffusivity (RD) abnormalities in tracts involved in primary and associative motor functions such as bilateral corticospinal tracts, the superior longitudinal fascicles, and the corpus callosum but also in nonmotor regions including the inferior fronto-occipital and longitudinal fascicles, cingulum bundles, anterior thalamic radiations, and uncinate fascicles. A combined tremor frequency and amplitude score correlated with RD and MD in extensive WM areas, which partially overlapped the regions that were associated with tremor frequency. No significant relationship was found between DTI measures and clinical rating scales scores. CONCLUSIONS: The results show that ET-related diffusion WM changes and their correlates with tremor severity are preferentially located in the primary and associative motor areas. In contrast, a relationship between WM was not detected with clinical rating scales. Accelerometry parameters may, therefore, serve as a potentially useful clinical measures that relate to WM deficits in ET.

Multi-institutional feasibility study of a fast patient localization method in total marrow irradiation with helical tomotherapy: a global health initiative by the international consortium of total marrow irradiation.

PURPOSE: To develop, characterize, and implement a fast patient localization method for total marrow irradiation. METHODS AND MATERIALS: Topographic images were acquired using megavoltage computed tomography (MVCT) detector data by delivering static orthogonal beams while the couch traversed through the gantry. Geometric and detector response corrections were performed to generate a megavoltage topogram (MVtopo). We also generated kilovoltage topograms (kVtopo) from the projection data of 3-dimensional CT images to reproduce the same geometry as helical tomotherapy. The MVtopo imaging dose and the optimal image acquisition parameters were investigated. A multi-institutional phantom study was performed to verify the image registration uncertainty. Forty-five MVtopo images were acquired and analyzed with in-house image registration software. RESULTS: The smallest jaw size (front and backup jaws of 0) provided the best image contrast and longitudinal resolution. Couch velocity did not affect the image quality or geometric accuracy. The MVtopo dose was less than the MVCT dose. The image registration uncertainty from the multi-institutional study was within 2.8 mm. In patient localization, the differences in calculated couch shift between the registration with MVtopo-kVtopo and MVCT-kVCT images in lateral, cranial-caudal, and vertical directions were 2.2 ± 1.7 mm, 2.6 ± 1.4 mm, and 2.7 ± 1.1 mm, respectively. The imaging time in MVtopo acquisition at the couch speed of 3 cm/s was <1 minute, compared with ≥15 minutes in MVCT for all patients. CONCLUSION: Whole-body MVtopo imaging could be an effective alternative to time-consuming MVCT for total marrow irradiation patient localization.

New light-amplifier-based detector designs for high spatial resolution and high sensitivity CBCT mammography and fluoroscopy.

New cone-beam computed tomographic (CBCT) mammography system designs are presented where the detectors provide high spatial resolution, high sensitivity, low noise, wide dynamic range, negligible lag and high frame rates similar to features required for high performance fluoroscopy detectors. The x-ray detectors consist of a phosphor coupled by a fiber-optic taper to either a high gain image light amplifier (LA) then CCD camera or to an electron multiplying CCD. When a square-array of such detectors is used, a field-of-view (FOV) to 20 × 20 cm can be obtained where the images have pixel-resolution of 100 µm or better. To achieve practical CBCT mammography scan-times, 30 fps may be acquired with quantum limited (noise free) performance below 0.2 µR detector exposure per frame. Because of the flexible voltage controlled gain of the LA's and EMCCDs, large detector dynamic range is also achievable. Features of such detector systems with arrays of either generation 2 (Gen 2) or 3 (Gen 3) LAs optically coupled to CCD cameras or arrays of EMCCDs coupled directly are compared. Quantum accounting analysis is done for a variety of such designs where either the lowest number of information carriers off the LA photo-cathode or electrons released in the EMCCDs per x-ray absorbed in the phosphor are large enough to imply no quantum sink for the design. These new LA- or EMCCD-based systems could lead to vastly improved CBCT mammography, ROI-CT, or fluoroscopy performance compared to systems using flat panels.

Experimental comparison of cone beam CT (CBCT) reconstruction and multi-view reconstruction (MVR) for microangiography (MA) detector system.

The new Multi-View Reconstruction (MVR) method for generating 3D vascular images was evaluated experimentally. The MVR method requires only a few digital subtraction angiographic (DSA) projections to reconstruct the 3D model of the vessel object compared to 180 or more projections for standard CBCT. Full micro-CBCT datasets of a contrast filled carotid vessel phantom were obtained using a Microangiography (MA) detector. From these datasets, a few projections were selected for use in the MVR technique. Similar projection views were also obtained using a standard x-ray image intensifier (II) system. A comparison of the 2D views of the MVRs (MA and II derived) with reference micro-CBCT data, demonstrated best agreement with the MA MVRs, especially at the curved part of the phantom. Additionally, the full 3D MVRs were compared with the full micro-CBCT 3D reconstruction resulting for the phantom with the smallest diameter (0.75 mm) vessel, in a mean centerline deviation from the micro-CBCT derived reconstructions of 29 µm for the MA MVR and 48 µm for the II MVR. The comparison implies that an MVR may be substituted for a full micro-CBCT scan for evaluating vessel segments with consequent substantial savings in patient exposure and contrast media injection yet without substantial loss in 3D image content. If a high resolution system with MA detector is used, the improved resolution could be well suited for endovascular image guided interventions where visualization of only a small field of view (FOV) is required.