Software for browsing sectioned images of a dog body and generating a 3D model

The goals of this study were (1) to provide accessible and instructive browsing software for sectioned images and a portable document format (PDF) file that includes three‐dimensional (3D) models of an entire dog body and (2) to develop techniques for segmentation and 3D modeling that would enable an investigator to perform these tasks without the aid of a computer engineer. To achieve these goals, relatively important or large structures in the sectioned images were outlined to generate segmented images. The sectioned and segmented images were then packaged into browsing software. In this software, structures in the sectioned images are shown in detail and in real color. After 3D models were made from the segmented images, the 3D models were exported into a PDF file. In this format, the 3D models could be manipulated freely. The browsing software and PDF file are available for study by students, for lecture for teachers, and for training for clinicians. These files will be helpful for anatomical study by and clinical training of veterinary students and clinicians. Furthermore, these techniques will be useful for researchers who study two‐dimensional images and 3D models. Anat Rec, 299:81–87, 2016. © 2015 Wiley Periodicals, Inc.     

Accessible and Informative Sectioned Images,Color‐Coded Images,and Surface Models of the Ear

In our previous research, we created state‐of‐the‐art sectioned images, color‐coded images, and surface models of the human ear. Our ear data would be more beneficial and informative if they were more easily accessible. Therefore, the purpose of this study was to distribute the browsing software and the PDF file in which ear images are to be readily obtainable and freely explored. Another goal was to inform other researchers of our methods for establishing the browsing software and the PDF file. To achieve this, sectioned images and color‐coded images of ear were prepared (voxel size 0.1 mm). In the color‐coded images, structures related to hearing, equilibrium, and structures originated from the first and second pharyngeal arches were segmented supplementarily. The sectioned and color‐coded images of right ear were added to the browsing software, which displayed the images serially along with structure names. The surface models were reconstructed to be combined into the PDF file where they could be freely manipulated. Using the browsing software and PDF file, sectional and three‐dimensional shapes of ear structures could be comprehended in detail. Furthermore, using the PDF file, clinical knowledge could be identified through virtual otoscopy. Therefore, the presented educational tools will be helpful to medical students and otologists by improving their knowledge of ear anatomy. The browsing software and PDF file can be downloaded without charge and registration at our homepage ( http://anatomy.dongguk.ac.kr/ear/ ). Anat Rec, 2013. © 2013 Wiley Periodicals, Inc.     

Advanced features of whole body sectioned images: Virtual Chinese Human

Serially sectioned images of whole cadavers have become available through the work of four projects: the Visible Human Project, the Visible Korean, the Chinese Visible Human, and the Virtual Chinese Human (VCH). For the VCH, new techniques and equipment were developed and applied to two female and two male cadavers to overcome some of the limitations noted in previous studies. In this article on the VCH, the procedures described are those used on a male cadaver. The cadaver was young with little to no pathology; there were no flat back artifacts because the cadaver was frozen and embedded in the upright position. Sectioned images (intervals, 0.2 mm) were of exceptional quality and resolution (0.1 mm‐sized pixels). Several specific structures were outlined (intervals, 0.6 mm) to acquire segmented images, from which surface models were constructed. The VCH data are to be distributed worldwide and are expected to encourage other investigators to produce useful three‐dimensional images and develop interactive simulation programs for clinical practice. Clin. Anat. 23:523–529, 2010. © 2010 Wiley‐Liss, Inc.     

3D printing of MRI compatible components: Why every MRI research group should have a low-budget 3D printer

PurposeTo evaluate low budget 3D printing technology to create MRI compatible components.Material and methodsA 3D printer is used to create customized MRI compatible components, a loop-coil platform and a multipart mouse fixation. The mouse fixation is custom fit for a dedicated coil and facilitates head fixation with bite bar, anesthetic gas supply and biomonitoring sensors. The mouse fixation was tested in a clinical 3T scanner.ResultsAll parts were successfully printed and proved MR compatible. Both design and printing were accomplished within a few days and the final print results were functional with well defined details and accurate dimensions (Δ <  0.4 mm). MR images of the mouse head clearly showed reduced motion artifacts, ghosting and signal loss when using the fixation.ConclusionsWe have demonstrated that a low budget 3D printer can be used to quickly progress from a concept to a functional device at very low production cost. While 3D printing technology does impose some restrictions on model geometry, additive printing technology can create objects with complex internal structures that can otherwise not be created by using lathe technology. Thus, we consider a 3D printer a valuable asset for MRI research groups.     

Segmentation accuracy of long bones

The use of three-dimensional imaging methodologies in new applications in the orthopaedic field has introduced a need for high accuracy, in addition to a correct diagnosis. The aim of this study was to quantify the absolute dimensional errors between models reconstructed from computed tomography and magnetic resonance images compared to a ground truth for various regions of the bone. Clinical CT and MRI scans were acquired from nine lower leg cadavers and the bones were subsequently cleaned from soft tissues. 3D models of the tibia were created from the segmented CT and MRI images and compared to optical scans of the cleaned bones (considered as ground truth). The 3D reconstruction using CT images resulted in an RMS error of 0.55 mm, corresponding to an overestimated CT bone model compared to the cleaned bone. MR imaging resulted in an RMS error of 0.56 mm; however, the MRI bone model was on average a small underestimation of the cleaned bone. Different regions of the bones were analysed, indicating a difference in accuracy between diaphysis and epiphysis. This study demonstrates a high accuracy for both CT and MRI imaging, supporting the feasibility of using MRI technology for the 3D reconstruction of bones in medical applications.     

Accuracy of model-based tracking of knee kinematics and cartilage contact measured by dynamic volumetric MRI

The purpose of this study was to determine the accuracy of knee kinematics and cartilage contact measured by volumetric dynamic MRI. A motor-actuated phantom drove femoral and tibial bone segments through cyclic 3D motion patterns. Volumetric images were continuously acquired using a 3D radially undersampled cine spoiled gradient echo sequence (SPGR-VIPR). Image data was binned based on position measured via a MRI-compatible rotary encoder. High-resolution static images were segmented to create bone models. Model-based tracking was performed by optimally registering the bone models to the volumetric images at each frame of the SPGR-VIPR series. 3D tibiofemoral translations and orientations were reconstructed, and compared to kinematics obtained by tracking fiducial markers. Imaging was repeated on a healthy subject who performed cyclic knee flexion-extension. Cartilage contact for the subject was assessed by measuring the overlap between articular cartilage surfaces. Model-based tracking was able to track tibiofemoral angles and translations with precisions less than 0.8° and 0.5 mm. These precisions resulted in an uncertainty of less than 0.5 mm in cartilage contact location. Dynamic SPGR-VIPR imaging can accurately assess in vivo knee kinematics and cartilage contact during voluntary knee motion performed in a MRI scanner. This technology could facilitate the quantitative investigation of links between joint mechanics and the development of osteoarthritis.     

Segmentation and Surface Reconstruction of the Detailed Ear Structures,Identified in Sectioned Images

The structure of the ear, which intervenes between gross anatomy and histology in size, can be best understood by means of three‐dimensional (3D) surface models on a computer. Furthermore, surface models are the source of interactive simulation for clinical trials, such as tympanoplasty. The objective of this research was to elaborate the surface models of detailed ear structures, which contribute to learning anatomy or the practice of otology. We produced sectioned images of a cadaver head (pixel size, 0.1 mm; 48‐bit color). In the sectioned images, the external, middle, and internal ear structures and other related components were delineated on Photoshop to acquire segmented images at 0.5‐mm intervals. Segmented images of each structure were stacked, and the surface was reconstructed to generate a 3D‐surface model on commercial software. Thirty surface models showed fine ear topographic anatomy (e.g., semicircular ducts), as expected. Herein, we present the corresponding sectioned images, segmented images, and surface models of ear structures that will be released together. It is hoped that these image data will stimulate the development of medical simulations. The efficient technique of segmentation and surface reconstruction enables the manufacture of surface models from other serial images (e.g., CTs and MRIs). Anat Rec, 2011. © 2011 Wiley‐Liss, Inc.     

Dynamic imaging with dual-source gated Computed Tomography (CT): Implications of motion parameters on image quality for wrist imaging

ObjectiveDynamic Computed Tomography (CT) promises insights into the pathophysiology of carpal instability by recording images of the carpus while it is in motion. The purpose of this study was to investigate the effect of motion velocity on image quality for dynamic carpal imaging applications using a clinical dual-source CT (DSCT) scanner.MethodsA phantom with targets in the axial, coronal and sagittal planes was attached to a motion simulator and imaged using a 64-slice DSCT scanner. Data was acquired when the phantom was stationary and during periodic linear motion. Spatial resolution, motion artifacts and banding artifacts were assessed.ResultsMean spatial resolution was 0.82 mm at 36 mm/s and 0.79 mm at 18 mm/s. Banding artifacts were mild at 36 mm/s and minimal at 18 mm/s. Motion artifacts were minimal at motion velocity of up to 36 mm/s in both the coronal and sagittal planes. Axial plane motion artifacts were moderate at 36 mm/s and mild at 18 mm/s.DiscussionSub-millimeter resolution is achievable with commercially available DSCT scanners with mild to moderate amounts of motion artifacts at velocities of 18 mm/s and 36 mm/s respectively.     

The quality of bone surfaces may govern the use of model based fluoroscopy in the determination of joint laxity

The assessment of knee joint laxity is clinically important but its quantification remains elusive. Calibrated, low dosage fluoroscopy, combined with registered surfaces and controlled external loading may offer possible solutions for quantifying relative tibio-femoral motion without soft tissue artefact, even in native joints. The aim of this study was to determine the accuracy of registration using CT and MRI derived 3D bone models, as well as metallic implants, to 2D single-plane fluoroscopic datasets, to assess their suitability for examining knee joint laxity.Four cadaveric knees and one knee implant were positioned using a micromanipulator. After fluoroscopy, the accuracy of registering each surface to the 2D fluoroscopic images was determined by comparison against known translations from the micromanipulator measurements. Dynamic measurements were also performed to assess the relative tibio-femoral error. For CT and MRI derived 3D femur and tibia models during static testing, the in-plane error was 0.4 mm and 0.9 mm, and out-of-plane error 2.6 mm and 9.3 mm respectively. For metallic implants, the in-plane error was 0.2 mm and out-of-plane error 1.5 mm. The relative tibio-femoral error during dynamic measurements was 0.9 mm, 1.2 mm and 0.7 mm in-plane, and 3.9 mm, 10.4 mm and 2.5 mm out-of-plane for CT and MRI based models and metallic implants respectively. The rotational errors ranged from 0.5° to 1.9° for CT, 0.5–4.3° for MRI and 0.1–0.8° for metallic implants.The results of this study indicate that single-plane fluoroscopic analysis can provide accurate information in the investigation of knee joint laxity, but should be limited to static or quasi-static evaluations when assessing native bones, where possible. With this knowledge of registration accuracy, targeted approaches for the determination of tibio-femoral laxity could now determine objective in vivo measures for the identification of ligament reconstruction candidates as well as improve our understanding of the consequences of knee joint instability in TKA.     

In-vitro validation of a non-invasive dual fluoroscopic imaging technique for measurement of the hip kinematics

Measurement of accurate in vivo hip joint kinematics in 6-DOF is difficult. Few studies have reported non-invasive measurements of the hip kinematics. The objective of this study was to validate a non-invasive dual fluoroscopic imaging system (DFIS) for measurement of hip kinematics. Bi-lateral hip joints of a cadaveric pelvic specimen were CT scanned to create bone models of the femur and pelvis, and subsequently tested in static and dynamic conditions inside the DFIS. The poses of the hip in space were then determined by matching the bone models with the fluoroscopic images. The pose data was compared to those obtained using a radio-stereometric analysis to determine the accuracy of the DFIS. The accuracy ± precision for measuring the hip kinematics were less than 0.93 ± 1.13 mm for translations and 0.59 ± 0.82° for rotations in all conditions. The repeatability of the DFIS technique was less than ±0.77 mm and ±0.64° in position and orientation for measuring hip kinematics in both static and dynamic positions. This technique could thus be a promising tool for determining 6-DOF poses of the hip during functional activities, which may help to understand biomechanical factors in hip pathologic conditions such as osteoarthritis and femoroacetabular impingement before and after surgical treatment.     

Fibre orientation of fresh and frozen porcine aorta determined non-invasively using diffusion tensor imaging

Diffusion tensor imaging analysis was applied to fresh and frozen porcine aortas in order to determine fibre orientation. Fresh and stored frozen porcine aortas were imaged in a 7 T scanner with a diffusion weighted spin echo sequence (six gradient directions, matrix 128 × 128 pixels, 2.8 cm × 2.8 cm field of view). The images were taken for different b values, ranging from 200 s/mm² to 1600 s/mm². For each dataset the diffusion tensor was evaluated, fractional anisotropy (FA) maps were calculated, and the fibres mapped. The arterial fibres resulting were postprocessed and their fibre angle evaluated. The FA maps, the dominant fibre angle, and the fibre pattern in the arterial wall thickness were compared in the fresh and in the stored frozen aortas. The technique was able to determine a fibre pattern in the fresh healthy aorta that is in accordance with the data available in literature and to identify an alteration in the fibre pattern caused by freezing. This study shows that this technique has potential for studying fibre orientation and fibre distribution in humans and could be further developed to diagnose fibre alterations due to cardiovascular diseases. In fact, our results suggest that DTI has the potential to determine the fibrous structure of arteries non-invasively. This capability could be further developed to study the natural remodelling of the aorta in vivo due to age and/or gender or to obtain information on aortic diseases at an early stage of their evolution.     

Spinal cerebrospinal fluid leaks detected by radionuclide cisternography and magnetic resonance imaging in patients suspected of intracranial hypotension

PurposeAlthough many studies have described various features of neuroimaging tests associated with intracranial hypotension, few have examined their validity and reliability. We evaluated the association between CSF leaks detected by radionuclide cisternography and abnormal MRI findings in the accurate diagnosis of intracranial hypotension.Patients/methodsWe retrospectively assessed 250 patients who were suspected of intracranial hypotension and underwent subsequent radionuclide cisternography. We obtained 159 sagittal and 153 coronal T2-weighted MRI images and 101 gadolinium-enhanced T1-weighted MRI images. We assessed the CSF leaks in relation to a sagging brain, the maximum subdural space in sagittal and coronal images, and dural enhancement.ResultsOverall, 186 (74%) patients showed CSF leaks on radionuclide cisternography. A sagging brain was observed in 21 (13%) of the 159 patients with sagittal MRIs. A sagging brain was not associated with CSF leaks (14% vs. 10%; p = 0.49). Compared to patients without CSF leaks, those with CSF leaks tended to have a larger maximum subdural space in both the sagittal (3.7 vs. 4.1 mm) and coronal (2.5 vs. 2.8 mm) images; however, the differences were not significant (p = 0.18 and p = 0.53, respectively). Dural enhancement was observed only in one patient, who presented with CSF leaks on radionuclide cisternography.ConclusionsOur study, which included a relatively large population, did not find any association between the findings of radionuclide cisternography and MRI. Future research should focus on identifying more valid neuroimaging findings to diagnose intracranial hypotension accurately.     

A multi-tissue mass-spring model for computer assisted breast surgery

The aim of this work was to develop and validate a 3D female breast deformation model for computer assisted breast surgery. Magnetic resonance (MR) image data of a patient undergoing breast biopsy, were acquired using two different protocols with the patient in prone position: (i) uncompressed breast and (ii) compressed breast, with lateral single breast compression, realized with a movable slab. The acquired images were then segmented using a semi-automatic procedure and from the extracted volumes of interest tetrahedral meshes representing skin, fat and mammary glands were generated. Tissue deformation was ruled by a mass-spring model: first, an iterative approximation algorithm was implemented to estimate the spring's rest length and stiffness, accounting for gravity force; then the resulting parameters were used to deform the uncompressed breast model in order to reach the real compressed one (ground truth). Results showed that gravity force applied to the mesh was properly compensated by the internal elastic forces, leading to a distance between the deformed mesh and the reference data of 0.036 ± 0.092 mm (median ± inter quartile range). The point to mesh residual distance between the deformed mesh and the ground truth was 1.224 ± 2.202 mm (median ± inter quartile range). Further investigation on a larger patient dataset is required for a more robust confirmation of model accuracy in predicting breast deformations.     

Cement penetration after patella venting

There is a high rate of patellofemoral complications following total knee arthroplasty. Optimization of the cement–bone interface by venting and suction of the tibial plateau has been shown to improve cement penetration. Our study was designed to investigate if venting the patella prior to cementing improved cement penetration.Ten paired cadaver patellae were allocated prior to resurfacing to be vented or non-vented. Bone mineral density (BMD) was measured by DEXA scanning. In vented specimens, a 1.6 mm Kirschner wire was used to breach the anterior cortex at the center. Specimens were resurfaced with standard Profix instrumentation and Versabond bone cement (Smith and Nephew PLC, UK). Cement penetration was assessed from Faxitron and sectioned images by a digital image software package (ImageJ V1.38, NIH, USA). Wilcoxon rank sum test was used to assess the difference in cement penetration between groups. The relationship between BMD and cement penetration was analyzed by Pearson correlation coefficient.There was a strong negative correlation between peak BMD and cement penetration when analyzed independent of experimental grouping (r² = ? 0.812, p = 0.004). Wilcoxon rank sum testing demonstrated no significant difference (rank sum statistic W = 27, p = 0.579) in cement penetration between vented (10.53% ± 4.66; mean ± std dev) and non-vented patellae (11.51% ± 6.23; mean ± std dev). Venting the patella using a Kirschner wire does not have a significant effect on the amount of cement penetration achieved in vitro using Profix instrumentation and Versabond cement.     

The influence of elastic upstream artery length on fluid–structure interaction modeling: A comparative study using patient-specific cerebral aneurysm

Fluid–structure interaction (FSI) simulations using a patient-specific geometry are carried out to investigate the influence the length of elastic parent artery and the position of constraints in the solid domain on the accuracy of patient-specific FSI simulations. Three models are tested: Long, Moderate, and Short, based on the length of the elastic parent artery. All three models use same wall thickness (0.5 mm) and the elastic modulus (5 MPa). The maximum mesh displacement is the largest for the Long model (0.491 mm) compared to other models (0.3 mm for Moderate, and 0.132 mm for Short). The differences of hemodynamic and mechanical variables, aneurysm volume and cross-sectional area between three models are all found to be minor. In addition, the Short model takes the least amount of computing time of the three models (11 h compared to 21 h for Long and 19 h for Moderate). The present results indicate that the use of short elastic upstream artery can shorten the time required for patient-specific FSI simulations without impacting the overall accuracy of the results.     

An SEMG computer interface using three myoelectric sites for proportional two-dimensional cursor motion control and clicking for individuals with spinal cord injuries

We developed an alternative computer interface using surface electromyography (sEMG) for individuals with spinal cord injuries (SCI) to access a computer. We designed this interface to make a cursor move on a two-dimensional screen and to click using only three muscles for each subject. In addition, a user can voluntarily control cursor movement speed by modulating muscle contraction levels. Three SCI patients and 10 healthy subjects volunteered to evaluate the performance of this interface using Fitts’ law test in a two-dimensional testing setup. The throughputs (TP) of our interface were 0.1962 ± 0.0562 b/s for the SCI patients and 0.4356 ± 0.0706 b/s for the healthy subjects. This interface could help SCI patients handle a wider range of activities such as browsing the Internet and communicating with others.     

Correction of step artefact associated with MRI scanning of long bones

3D models of long bones are being utilised for a number of fields including orthopaedic implant design. Accurate reconstruction of 3D models is of utmost importance to design accurate implants to allow achieving a good alignment between two bone fragments. Thus for this purpose, CT scanners are employed to acquire accurate bone data exposing an individual to a high amount of ionising radiation. Magnetic resonance imaging (MRI) has been shown to be a potential alternative to computed tomography (CT) for scanning of volunteers for 3D reconstruction of long bones, essentially avoiding the high radiation dose from CT. In MRI imaging of long bones, the artefacts due to random movements of the skeletal system create challenges for researchers as they generate inaccuracies in the 3D models generated by using data sets containing such artefacts.One of the defects that have been observed during an initial study is the lateral shift artefact occurring in the reconstructed 3D models. This artefact is believed to result from volunteers moving the leg during two successive scanning stages (the lower limb has to be scanned in at least five stages due to the limited scanning length of the scanner). As this artefact creates inaccuracies in the implants designed using these models, it needs to be corrected before the application of 3D models to implant design. Therefore, this study aimed to correct the lateral shift artefact using 3D modelling techniques.The femora of five ovine hind limbs were scanned with a 3T MRI scanner using a 3D vibe based protocol. The scanning was conducted in two halves, while maintaining a good overlap between them. A lateral shift was generated by moving the limb several millimetres between two scanning stages. The 3D models were reconstructed using a multi threshold segmentation method. The correction of the artefact was achieved by aligning the two halves using the robust iterative closest point (ICP) algorithm, with the help of the overlapping region between the two. The models with the corrected artefact were compared with the reference model generated by CT scanning of the same sample.The results indicate that the correction of the artefact was achieved with an average deviation of 0.32 ± 0.02 mm between the corrected model and the reference model. In comparison, the model obtained from a single MRI scan generated an average error of 0.25 ± 0.02 mm when compared with the reference model. An average deviation of 0.34 ± 0.04 mm was seen when the models generated after the table was moved were compared to the reference models; thus, the movement of the table is also a contributing factor to the motion artefacts.     

The virtual dissecting room: Creating highly detailed anatomy models for educational purposes

IntroductionVirtual 3D models are powerful tools for teaching anatomy. At the present day, there are a lot of different digital anatomy models, most of these commercial applications are based on a 3D model of a human body reconstructed from images with a 1 mm intervals. The use of even smaller intervals may result in more details and more realistic appearances of 3D anatomy models. The aim of this study was to create a realistic and highly detailed 3D model of the hand and wrist based on small interval cross-sectional images, suitable for undergraduate and postgraduate teaching purposes with the possibility to perform a virtual dissection in an educational application.MethodsIn 115 transverse cross-sections from a human hand and wrist, segmentation was done by manually delineating 90 different structures. With the use of Amira the segments were imported and a surface model/polygon model was created, followed by smoothening of the surfaces in Mudbox. In 3D Coat software the smoothed polygon models were automatically retopologied into a quadrilaterals formation and a UV map was added. In Mudbox, the textures from 90 structures were depicted in a realistic way by using photos from real tissue and afterwards height maps, gloss and specular maps were created to add more level of detail and realistic lightning on every structure. Unity was used to build a new software program that would support all the extra map features together with a preferred user interface.ConclusionA 3D hand model has been created, containing 100 structures (90 at start and 10 extra structures added along the way). The model can be used interactively by changing the transparency, manipulating single or grouped structures and thereby simulating a virtual dissection. This model can be used for a variety of teaching purposes, ranging from undergraduate medical students to residents of hand surgery. Studying the hand and wrist anatomy using this model is cost-effective and not hampered by the limited access to real dissecting facilities.     

Anatomic proximity of the peroneal nerve to the posterolateral corner of the knee determined by MR imaging

BackgroundThe pie crusting technique has been extensively used to release the lateral soft tissue in total knee arthroplasty. However, it may place the peroneal nerve at direct injury risk when performed in a valgus knee. The aim of this study was to determine the anatomic proximity of the peroneal nerve to the posterolateral corner of the knee.MethodsOne hundred knees were measured on axial MR images for the proximity of peroneal nerve to the closest edge of the inner surface of joint capsule or the posterolateral corner of proximal tibia at the level of the joint line and the level of the tibial cut respectively.ResultsThe distance between the peroneal nerve and the closest edge of the inner surface of joint capsule at the level of the joint line was 15.0 ± 2.6 mm (range, 8.5-22.3 mm), and the distance between the peroneal nerve and the posterolateral corner of proximal tibia was 14.0 ± 2.7 mm (range, 8.0-23.2 mm). These distances were correlated with the anteroposterior diameter of the soft tissue of the knee, but not correlated with the size of the tibia.ConclusionsThese results suggest that it is safe enough providing that the scalpel blade does not pierce more than 8 mm deep. However, patients with smaller legs are at greater risk of direct peroneal nerve injury.