Graph matching survey for medical imaging: On the way to deep learning.

The interest on graph matching has not stopped growing since the late seventies. The basic idea of graph matching consists of generating graph representations of different data or structures and compare those representations by searching correspondences between them. There are manifold techniques that have been developed to find those correspondences and the choice of one or another depends on the characteristics of the application of interest. These applications range from pattern recognition (e.g. biometric identification) to signal processing or artificial intelligence. One of the aspects that make graph matching so attractive is its ability to facilitate data analysis, and medical imaging is one of the fields that can benefit from this in a greater extent. The potential of graph matching to find similarities and differences between data acquired at different points in time shows its potential to improve diagnosis, follow-up of human diseases or any other of the clinical scenarios that require comparison between different datasets. In spite of the large amount of papers that were published in this field to the date there is no survey paper of graph matching for clinical applications. This survey aims to fill this gap.

PupilEXT: Flexible Open-Source Platform for High-Resolution Pupillometry in Vision Research.

The human pupil behavior has gained increased attention due to the discovery of the intrinsically photosensitive retinal ganglion cells and the afferent pupil control path's role as a biomarker for cognitive processes. Diameter changes in the range of 10-2 mm are of interest, requiring reliable and characterized measurement equipment to accurately detect neurocognitive effects on the pupil. Mostly commercial solutions are used as measurement devices in pupillometry which is associated with high investments. Moreover, commercial systems rely on closed software, restricting conclusions about the used pupil-tracking algorithms. Here, we developed an open-source pupillometry platform consisting of hardware and software competitive with high-end commercial stereo eye-tracking systems. Our goal was to make a professional remote pupil measurement pipeline for laboratory conditions accessible for everyone. This work's core outcome is an integrated cross-platform (macOS, Windows and Linux) pupillometry software called PupilEXT, featuring a user-friendly graphical interface covering the relevant requirements of professional pupil response research. We offer a selection of six state-of-the-art open-source pupil detection algorithms (Starburst, Swirski, ExCuSe, ElSe, PuRe and PuReST) to perform the pupil measurement. A developed 120-fps pupillometry demo system was able to achieve a calibration accuracy of 0.003 mm and an averaged temporal pupil measurement detection accuracy of 0.0059 mm in stereo mode. The PupilEXT software has extended features in pupil detection, measurement validation, image acquisition, data acquisition, offline pupil measurement, camera calibration, stereo vision, data visualization and system independence, all combined in a single open-source interface, available at https://github.com/openPupil/Open-PupilEXT.

Leveraging spatial uncertainty for online error compensation in EMT.

PURPOSE: Electromagnetic tracking (EMT) can potentially complement fluoroscopic navigation, reducing radiation exposure in a hybrid setting. Due to the susceptibility to external distortions, systematic error in EMT needs to be compensated algorithmically. Compensation algorithms for EMT in guidewire procedures are only practical in an online setting. METHODS: We collect positional data and train a symmetric artificial neural network (ANN) architecture for compensating navigation error. The results are evaluated in both online and offline scenarios and are compared to polynomial fits. We assess spatial uncertainty of the compensation proposed by the ANN. Simulations based on real data show how this uncertainty measure can be utilized to improve accuracy and limit radiation exposure in hybrid navigation. RESULTS: ANNs compensate unseen distortions by more than 70%, outperforming polynomial regression. Working on known distortions, ANNs outperform polynomials as well. We empirically demonstrate a linear relationship between tracking accuracy and model uncertainty. The effectiveness of hybrid tracking is shown in a simulation experiment. CONCLUSION: ANNs are suitable for EMT error compensation and can generalize across unseen distortions. Model uncertainty needs to be assessed when spatial error compensation algorithms are developed, so that training data collection can be optimized. Finally, we find that error compensation in EMT reduces the need for X-ray images in hybrid navigation.

High-precision evaluation of electromagnetic tracking.

PURPOSE: Navigation in high-precision minimally invasive surgery (HP-MIS) demands high tracking accuracy in the absence of line of sight (LOS). Currently, no tracking technology can satisfy this requirement. Electromagnetic tracking (EMT) is the best tracking paradigm in the absence of LOS despite limited accuracy and robustness. Novel evaluation protocols are needed to ensure high-precision and robust EMT for navigation in HP-MIS. METHODS: We introduce a novel protocol for EMT measurement evaluation featuring a high-accuracy phantom based on LEGO[Formula: see text], which is calibrated by a coordinate measuring machine to ensure accuracy. Our protocol includes relative sequential positions and an uncertainty estimation of positioning. We show effects on distortion compensation using a learned interpolation model. RESULTS: Our high-precision protocol clarifies properties of errors and uncertainties of EMT for high-precision use cases. For EMT errors reaching clinically relevant 0.2 mm, our design is 5-10 times more accurate than previous protocols with 95% confidence margins of 0.02 mm. This high-precision protocol ensures the performance improvement in compensated EMT by 0.05 mm. CONCLUSION: Our protocol improves the reliability of EMT evaluations because of significantly lower protocol-inherent uncertainties. To reduce patient risk in HP-MIS and to evaluate magnetic field distortion compensation, more high-accuracy protocols such as the one proposed here are required.

Planning nonlinear access paths for temporal bone surgery.

PURPOSE: Interventions at the otobasis operate in the narrow region of the temporal bone where several highly sensitive organs define obstacles with minimal clearance for surgical instruments. Nonlinear trajectories for potential minimally invasive interventions can provide larger distances to risk structures and optimized orientations of surgical instruments, thus improving clinical outcomes when compared to existing linear approaches. In this paper, we present fast and accurate planning methods for such nonlinear access paths. METHODS: We define a specific motion planning problem in [Formula: see text] with notable constraints in computation time and goal pose that reflect the requirements of temporal bone surgery. We then present [Formula: see text]-RRT-Connect: two suitable motion planners based on bidirectional Rapidly exploring Random Tree (RRT) to solve this problem efficiently. RESULTS: The benefits of [Formula: see text]-RRT-Connect are demonstrated on real CT data of patients. Their general performance is shown on a large set of realistic synthetic anatomies. We also show that these new algorithms outperform state-of-the-art methods based on circular arcs or Bézier-Splines when applied to this specific problem. CONCLUSION: With this work, we demonstrate that preoperative and intra-operative planning of nonlinear access paths is possible for minimally invasive surgeries at the otobasis.

Contrast-enhanced MR Imaging versus Contrast-enhanced US: A Comparison in Glioblastoma Surgery by Using Intraoperative Fusion Imaging.

Purpose To compare contrast material enhancement of glioblastoma multiforme (GBM) with intraoperative contrast-enhanced ultrasonography (US) versus that with preoperative gadolinium-enhanced T1-weighted magnetic resonance (MR) imaging by using real-time fusion imaging. Materials and Methods Ten patients with GBM were retrospectively identified by using routinely collected, anonymized data. Navigated contrast-enhanced US was performed after intravenous administration of contrast material before tumor resection. All patients underwent tumor excision with navigated intraoperative US guidance with use of fusion imaging between real-time intraoperative US and preoperative MR imaging. With use of fusion imaging, glioblastoma contrast enhancement at contrast-enhanced US (regarding location, morphologic features, margins, dimensions, and pattern) was compared with that at gadolinium-enhanced T1-weighted MR imaging. Results Fusion imaging for virtual navigation enabled matching of real-time contrast-enhanced US scans to corresponding coplanar preoperative gadolinium-enhanced T1-weighted MR images in all cases, with a positional discrepancy of less than 2 mm. Contrast enhancement of gadolinium-enhanced T1-weighted MR imaging and contrast-enhanced US was superimposable in all cases with regard to location, margins, dimensions, and morphologic features. The qualitative analysis of contrast enhancement pattern demonstrated a similar distribution in contrast-enhanced US and gadolinium-enhanced T1-weighted MR imaging in nine patients: Seven lesions showed peripheral inhomogeneous ring enhancement, and two lesions showed a prevalent nodular pattern. In one patient, the contrast enhancement pattern differed between the two modalities: Contrast-enhanced US showed enhancement of the entire bulk of the tumor, whereas gadolinium-enhanced T1-weighted MR imaging demonstrated peripheral contrast enhancement. Conclusion Glioblastoma contrast enhancement with contrast-enhanced US is superimposable on that provided with preoperative gadolinium-enhanced T1-weighted MR imaging regarding location, margins, morphologic features, and dimensions, with a similar enhancement pattern in most cases. Thus, contrast-enhanced US is of potential use in the surgical management of GBM. © RSNA, 2017 Online supplemental material is available for this article.

TOP: Prospective Evaluation of a Volume Based, Computer Assisted Method for Transperineal Optimized Prostate Biopsy.

OBJECTIVE: This study is a prospective evaluation of a volume-based, computer-assisted method for transperineal optimized prostate (TOP) biopsy. The TOP algorithm automates core planning for systematic prostate biopsies using the 3-dimensional organ contour and an alterable volume for tumors to be excluded. SUBJECTS AND METHODS: MRI-transrectal ultrasound fusion biopsy with MRI-targeted biopsies (TBs) and systematic-TOP biopsies were performed on 172 men between October 2013 and March 2014. Systematic biopsies were placed according to TOP for detection of tumor volumes >0.5 mL with a minimum of 80% organ coverage in prostates up to 50 mL (70% in larger organs). RESULTS: Median 24 TOP cores and 3 MRI-TBs have been placed. Prostate cancer (PCa) was detected in 112 of 172 (65%) of men; TOP detected 109 (97%) and TB 62 (55%). Significant cancer (Gleason score ≥7) was detected in 75 (44%) of men and of these TOP detected 73 of 75 (97%) and TB 51 of 75 (68%). Overall, systematic-TOP sampling significantly outperformed TB for the detection of both, all PCa as well as significant PCa (p < 0.0001, p = 0.0005). CONCLUSION: The TOP method is innovative by integrating the individual prostate volume and PCa volume detection thresholds. In the present cohort, it diagnosed more significant tumors than TB alone. However, at the same time, more low-risk tumors are detected.

Minimally invasive multiport surgery of the lateral skull base.

OBJECTIVE: Minimally invasive procedures minimize iatrogenic tissue damage and lead to a lower complication rate and high patient satisfaction. To date only experimental minimally invasive single-port approaches to the lateral skull base have been attempted. The aim of this study was to verify the feasibility of a minimally invasive multiport approach for advanced manipulation capability and visual control and develop a software tool for preoperative planning. METHODS: Anatomical 3D models were extracted from twenty regular temporal bone CT scans. Collision-free trajectories, targeting the internal auditory canal, round window, and petrous apex, were simulated with a specially designed planning software tool. A set of three collision-free trajectories was selected by skull base surgeons concerning the maximization of the distance to critical structures and the angles between the trajectories. RESULTS: A set of three collision-free trajectories could be successfully simulated to the three targets in each temporal bone model without violating critical anatomical structures. CONCLUSION: A minimally invasive multiport approach to the lateral skull base is feasible. The developed software is the first step for preoperative planning. Further studies will focus on cadaveric and clinical translation.

A novel stereotactic prostate biopsy system integrating pre-interventional magnetic resonance imaging and live ultrasound fusion.

PURPOSE: We developed an effective way to precisely diagnose prostate cancer using a novel prostate biopsy system that integrates pre-interventional magnetic resonance imaging with peri-interventional ultrasound for perineal navigated prostate biopsy. MATERIALS AND METHODS: A total of 106 men with findings suspicious for prostate cancer (median age 66 years, prostate specific antigen 8.0 ng/ml and prostate volume 47 ml) underwent multiparametric 3 Tesla magnetic resonance imaging. Suspicious lesions were marked and data were transferred to the novel biopsy system. Using a custom-made biplane transrectal ultrasound probe mounted on a stepper we gathered 3-dimensional ultrasound data and fused them with magnetic resonance imaging data. As a result, suspicious magnetic resonance imaging lesions were superimposed over the transrectal ultrasound data. Three-dimensional biopsy planning was done, including systematic biopsies. Perineal biopsies were taken under live ultrasound guidance and the precise site of each biopsy was documented in 3 dimensions. We evaluated feasibility, safety and cancer detection. RESULTS: Prostate cancer was detected in 63 of 106 patients (59.4%). Magnetic resonance imaging findings correlated positively with histopathology in 71 of 103 patients (68.9%). In magnetic resonance imaging lesions marked as highly suspicious, the detection rate was 95.8% (23 of 24 cases). Lesion targeted cores had a significantly higher positivity rate than nontargeted cores. The procedural targeting error of the first 2,461 biopsy cores was 1.7 mm. Regarding adverse effects, 2 patients experienced urinary retention and 1 had a perineal hematoma. Urinary tract infections did not develop. CONCLUSIONS: Perineal stereotactic prostate biopsies guided by the combination of magnetic resonance imaging and ultrasound enable effective examination of suspicious magnetic resonance imaging lesions. Each biopsy core taken is documented accurately for its location in 3 dimensions, enabling magnetic resonance imaging validation and tailored treatment planning. The morbidity of the procedure was minimal.

Patient positioning with X-ray detector self-calibration for image guided therapy.

Automatic alignment estimation from projection images has a range of applications, but misaligned cameras induce inaccuracies. Calibration methods for optical cameras requiring calibration bodies or detectable features have been a matter of research for years. Not so for image guided therapy, although exact patient pose recovery is crucial. To image patient anatomy, X-ray instead of optical equipment is used. Feature detection is often infeasible. Furthermore, a method not requiring a calibration body, usable during treatment, would be desirable to improve accuracy of the patient alignment. We present a novel approach not relying on image features but combining intensity based calibration with 3D pose recovery. A stereoscopic X-ray camera model is proposed, and effects of erroneous parameters on the patient alignment are evaluated. The relevant camera parameters are automatically computed by comparison of X-ray to CT images and are incorporated in the patient alignment computation. The methods were tested with ground truth data of an anatomic phantom with artificially produced misalignments and available real-patient images from a particle therapy machine. We show that our approach can compensate patient alignment errors through mis-calibration of a camera from more than 5 mm to below 0.2 mm. Usage of images with artificial noise shows that the method is robust against image degradation of 2-5%. X-ray camera self-calibration improves accuracy when cameras are misaligned. We could show that rigid body alignment was computed more accurately and that self-calibration is possible, even if detection of corresponding image features is not.

BiopSee® - transperineal stereotactic navigated prostate biopsy.

In the recent years, prostate cancer was the most commonly diagnosed cancer in men. Currently secure diagnosis confirmation is done by a transrectal biopsy and following histopathological examination. Conventional transrectal biopsy success rates are rather low with ca. 30% detection upon the first and ca 20% after re-biopsy. The paper presents a novel system for stereotactic navigated prostate biopsy. The approach results into higher accuracy, reproducibility and unrestricted and effective access to all prostate regions. Custom designed ultrasound, new template design and integrated 2-axes stepper allows superior 2D and 3D prostate imaging quality and precise needle navigation. DICOM functionality and image fusion enable to import pre-operative datasets (e.g. multiparametric MRI, targets etc.) and overlay all available radiological information into the biopsy planning and guiding procedure. The biopsy needle insertion itself is performed under augmented reality ultrasound guidance. Each procedure step is automatically documented in order to provide quality assurance and permit data re-usage for the further treatment. First clinical results indicates success rates of ca. 70% by first biopsies by our approach.

TraumaStation: a portable telemedicine station.

TraumaStation is a portable medical device which covers the mobility of the medical doctors as well as integrates the diversity of telemedicine devices. Many portable telemedicine devices has been developed the last years in order to help patients in remote areas or in emergency situationns. The medical TraumaStation is a light portable tele-medical first-aid device, which provides the physicians with an ultrasound, electrocardiogram, blood pressure, oxygen meter apparatus all in a suitcase. In addition, the portable device is equipped with all available telecommunication gateways (e.g. GSM, UMTS, ISDN, DSL, Satellite) providing a great communication convenience to the physicians utilizing XMMP instant messaging protocols and real time video conference.

Advantages and limitations of prospective head motion compensation for MRI using an optical motion tracking device.

RATIONALE AND OBJECTIVES: Subject motion appears to be a limiting factor in numerous magnetic resonance (MR) imaging (MRI) applications. In particular, head tremor, which often accompanies stroke, may render certain high-resolution two- (2D) and three-dimensional (3D) techniques inapplicable. The reason for that is head movement during acquisition. The study objective is to achieve a method able to compensate for complete motion during data acquisition. The method should be usable for every sequence and easily implemented on different MR scanners. MATERIALS AND METHODS: The possibility of interfacing the MR scanner with an external optical motion-tracking system capable of determining the object's position with submillimeter accuracy and an update rate of 60 Hz is shown. Movement information on the object position (head) is used to compensate for motion in real time by updating the field of view (FOV) by recalculating the gradients and radiofrequency parameter of the MR scanner during acquisition of k-space data, based on tracking data. RESULTS: Results of rotation phantom, in vivo experiments, and implementation of three different MRI sequences, 2D spin echo, 3D gradient echo, and echo planar imaging, are presented. Finally, the proposed method is compared with the prospective motion correction software available on the scanner software. CONCLUSION: A prospective motion correction method that works in real time only by updating the FOV of the MR scanner is presented. Results show the feasibility of using an external optical motion-tracking system to compensate for strong and fast subject motion during acquisition.

Integrated telemedicine applications and services for oncological positron emission tomography.

TENPET (Trans European Network for Positron Emission Tomography) aims to evaluate the provision of integrated teleconsultation and intelligent computer supported cooperative work services for clinical positron emission tomography (PET) in Europe at its current stage, as it is a multi-centre project financially supported by the European Commission (Information Society, eTEN Program). It addresses technological challenges by linking PET centres and developing supporting services that permit remote consultation between professionals in the field. The technological platform (CE-marked) runs on Win2000/NT/XP systems and incorporates advanced techniques for image visualization, analysis and fusion, as well as for interactive communication and message handling for off-line communications. Four PET Centres from Spain, France and Germany participate to the pilot system trials. The performance evaluation of the system is carried out via log files and user-filled questionnaires on the frequency of the teleconsultations, their duration and efficacy, quality of the images received, user satisfaction, as well as on privacy, ethical and security issues. TENPET promotes the co-operation and improved communication between PET practitioners that are miles away from their peers or on mobile units, offering options for second opinion and training and permitting physicians to remotely consult patient data if they are away from their centre. It is expected that TENPET will have a significant impact in the development of new skills by PET professionals and will support the establishment of peripheral PET units. To our knowledge, TENPET is the first telemedicine service specifically designed for oncological PET. This report presents the technical innovations incorporated in the TENPET platform and the initial pilot studies at real and diverse clinical environments in the field of oncology.

Accuracy of biopsy needle navigation using the Medarpa system--computed tomography reality superimposed on the site of intervention.

The aim of this work was to determine the accuracy of a new navigational system, Medarpa, with a transparent display superimposing computed tomography (CT) reality on the site of intervention. Medarpa uses an optical and an electromagnetic tracking system which allows tracking of instruments, the radiologist and the transparent display. The display superimposes a CT view of a phantom chest on a phantom chest model, in real time. In group A, needle positioning was performed using the Medarpa system. Three targets (diameter 1.5 mm) located inside the phantom were punctured. In group B, the same targets were used to perform standard CT-guided puncturing using the single-slice technique. The same needles were used in both groups (15 G, 15 cm). A total of 42 punctures were performed in each group. Post puncture, CT scans were made to verify needle tip positions. The mean deviation from the needle tip to the targets was 6.65+/-1.61 mm for group A (range 3.54-9.51 mm) and 7.05+/-1.33 mm for group B (range 4.10-9.45 mm). No significant difference was found between group A and group B for any target (p>0.05). No significant difference was found between the targets of the same group (p>0.05). The accuracy in needle puncturing using the augmented reality system, Medarpa, matches the accuracy achieved by CT-guided puncturing technique.

Prospective head motion compensation for MRI by updating the gradients and radio frequency during data acquisition.

Subject motion appears to be a limiting factor in numerous magnetic resonance imaging (MRI) applications. For head imaging the subject's ability to maintain the same head position for a considerable period of time places restrictions on the total acquisition time. For healthy individuals this time typically does not exceed 10 minutes and may be considerably reduced in case of pathology. In particular, head tremor, which often accompanies stroke, may render certain high-resolution 2D and 3D techniques inapplicable. Several navigator techniques have been proposed to circumvent the subject motion problem. The most suitable for head imaging appears to be the orbital or spherical navigator methods. Navigators, however, not only lengthen the measurement because of the time required for acquisition of the position information, but also require additional excitation radio frequency (RF) pulses to be incorporated into the sequence timing, which disturbs the steady state. Here we demonstrate the possibility of interfacing the MR scanner with an external optical motion tracking system, capable of determining the object's position with sub-millimeter accuracy and an update rate of 60Hz. The movement information on the object position (head) is used to compensate the motion in real time. This is done by updating the field of view (FOV) by recalculating the gradients and the RF-parameter of the MRI tomograph during the acquisition of k-space data based on the tracking data. Results of rotation phantom, in vivo experiments and the implementation in two different MRI sequences are presented.

The compensation of head motion artifacts using an infrared tracking system and a new algorithm for fMRI.

We aim to provide a next generation Magnetic Resonance Imaging (MRI) technology with an integrated solution for reducing motion artifacts in brain imaging applications. New developments in the field of MRI are revolutionizing the diagnostic capabilities e.g. of functional (fMRI) of the technique. Unfortunately, motion artifacts are eminent problems in cerebral MRI images, especially in difficult patient populations (e.g. chronic pain, children, neonates). Patient motion artifacts are present in 2D sequences, but are extremely detrimental in multi-slice 3D sequences often employed in fMRI. The problem of motion compensation in MRI technology deals with: Identification of the source as well as pattern of motion. Obtaining a mathematical model of motion that can be used to identify and then compensate the motion effects. Optimizing the image acquisition sequence in order to minimize, or even eliminate, the effect of motion. We propose a method to obtain a quantitative measure of the movement of the head between different data acquisition points in both MRI, and functional MRI examination.