Comparison of 2D vs. 3D U-Net Organ Segmentation in abdominal 3D CT images

A two-step concept for 3D segmentation on 5 abdominal organs inside volumetric CT images is presented. First each relevant organ's volume of interest is extracted as bounding box. The extracted volume acts as input for a second stage, wherein two compared U-Nets with different architectural dimensions re-construct an organ segmentation as label mask. In this work, we focus on comparing 2D U-Nets vs. 3D U-Net counterparts. Our initial results indicate Dice improvements of about 6\% at maximum. In this study to our surprise, liver and kidneys for instance were tackled significantly better using the faster and GPU-memory saving 2D U-Nets. For other abdominal key organs, there were no significant differences, but we observe highly significant advantages for the 2D U-Net in terms of GPU computational efforts for all organs under study.

3D Bounding Box Detection in Volumetric Medical Image Data: A Systematic Literature Review

This paper discusses current methods and trends for 3D bounding box detection in volumetric medical image data. For this purpose, an overview of relevant papers from recent years is given. 2D and 3D implementations are discussed and compared. Multiple identified approaches for localizing anatomical structures are presented. The results show that most research recently focuses on Deep Learning methods, such as Convolutional Neural Networks vs. methods with manual feature engineering, e.g. Random-Regression-Forests. An overview of bounding box detection options is presented and helps researchers to select the most promising approach for their target objects.

Robust GPU-based Virtual Reality Simulation of Radio Frequency Ablations for Various Needle Geometries and Locations

Purpose: Radio-frequency ablations play an important role in the therapy of malignant liver lesions. The navigation of a needle to the lesion poses a challenge for both the trainees and intervening physicians. Methods: This publication presents a new GPU-based, accurate method for the simulation of radio-frequency ablations for lesions at the needle tip in general and for an existing visuo-haptic 4D VR simulator. The method is implemented real-time capable with Nvidia CUDA. Results: It performs better than a literature method concerning the theoretical characteristic of monotonic convergence of the bioheat PDE and a in vitro gold standard with significant improvements (p < 0.05) in terms of Pearson correlations. It shows no failure modes or theoretically inconsistent individual simulation results after the initial phase of 10 seconds. On the Nvidia 1080 Ti GPU it achieves a very high frame rendering performance of >480 Hz. Conclusion: Our method provides a more robust and safer real-time ablation planning and intraoperative guidance technique, especially avoiding the over-estimation of the ablated tissue death zone, which is risky for the patient in terms of tumor recurrence. Future in vitro measurements and optimization shall further improve the conservative estimate.

Genaue modellbasierte Identifikation von gynäkologischen Katheterpfaden für die MRT-bildgestützte Brachytherapie

German text, english abstract: Mortality in gynecologic cancers, including cervical, ovarian, vaginal and vulvar cancers, is more than 6% internationally [1]. In many countries external radiotherapy is supplemented by brachytherapy with high locally administered doses as standard. The superior ability of magnetic resonance imaging (MRI) to differentiate soft tissue has led to an increasing use of this imaging technique in the intraoperative planning and implementation of brachytherapy. A technical challenge associated with the use of MRI imaging for brachytherapy - in contrast to computed tomography (CT) imaging - is the dark-diffuse appearance and thus difficult identification of the catheter paths in the resulting images. This problem is addressed by the precise method described herein of tracing the catheters from the catheter tip. The average identification time for a single catheter path was three seconds on a standard PC. Segmentation time, accuracy and precision are promising indicators of the value of this method for the clinical application of image-guided gynecological brachytherapy. After surgery (OP), the healthy surrounding tissue of the tumor is usually irradiated. This reduces the risk of leaving behind residual cells that would likely cause a recurrence of the cancer or the formation of metastases - secondary tumors elsewhere in the body. In the case of a tumor on the cervix or prostate, the operation is minimally invasive, ie. the removal of the cancer and the irradiation are performed cost-effectively and risk-avoiding by keyhole surgery instead of open surgery.

Population-based Respiratory 4D Motion Atlas Construction and its Application for VR Simulations of Liver Punctures

Virtual reality (VR) training simulators of liver needle insertion in the hepatic area of breathing virtual patients currently need 4D data acquisitions as a prerequisite. Here, first a population-based breathing virtual patient 4D atlas can be built and second the requirement of a dose-relevant or expensive acquisition of a 4D data set for a new static 3D patient can be mitigated by warping the mean atlas motion. The breakthrough contribution of this work is the construction and reuse of population-based learned 4D motion models.

Interpatient Respiratory Motion Model Transfer for Virtual Reality Simulations of Liver Punctures

Current virtual reality (VR) training simulators of liver punctures often rely on static 3D patient data and use an unrealistic (sinusoidal) periodic animation of the respiratory movement. Existing methods for the animation of breathing motion support simple mathematical or patient-specific, estimated breathing models. However with personalized breathing models for each new patient, a heavily dose relevant or expensive 4D data acquisition is mandatory for keyframe-based motion modeling. Given the reference 4D data, first a model building stage using linear regression motion field modeling takes place. Then the methodology shown here allows the transfer of existing reference respiratory motion models of a 4D reference patient to a new static 3D patient. This goal is achieved by using non-linear inter-patient registration to warp one personalized 4D motion field model to new 3D patient data. This cost- and dose-saving new method is shown here visually in a qualitative proof-of-concept study.

A New 3D Segmentation Technique for QCT Scans of the Lumbar Spine to Determine BMD and Vertebral Geometry

Quantitative computed tomography (QCT) is a standard method to determine bone mineral density (BMD) in the spine. Traditionally single 8 - 10 mm thick slices have been analyzed only. Current spiral CT scanners provide true 3D acquisition schemes allowing for a more differential BMD analysis and an assessment of geometric parameters, which may improve fracture prediction. We developed a novel 3D segmentation approach that combines deformable balloons, multi seeded volume growing, and dedicated morphological operations to extract the vertebral bodies. An anatomy-oriented coordinate system attached automatically to each vertebra is used to define volumes of interest. We analyzed intra-operator precision of the segmentation procedure using abdominal scans from 10 patients (60 mAs, 120 kV, slice thickness 1mm, B40s, Siemens Sensation 16). Our new segmentation method shows excellent precision errors in the order of < 1 % for BMD and < 2 % for volume.

A New 3D Method to Segment the Lumbar Vertebral Bodies and to Determine Bone Mineral Density and Geometry

In this paper we present a new 3D segmentation approach for the vertebrae of the lower thoracic and the lumbar spine in spiral computed tomography datasets. We implemented a multi-step procedure. Its main components are deformable models, volume growing, and morphological operations. The performance analysis that included an evaluation of accuracy using the European Spine Phantom, and of intra-operator precision using clinical CT datasets from 10 patients highlight the potential for clinical use. The intra-operator precision of the segmentation procedure was better than 1% for Bone Mineral Density (BMD) and better than 1.8% for volume. The long-term goal of this work is to enable better fracture prediction and improved patient monitoring in the field of osteoporosis. A true 3D segmentation also enables an accurate measurement of geometrical parameters that can augment the classical measurement of BMD.

A New 3D Segmentation Methodology for Lumbar Vertebral Bodies for the Measurement of BMD and Geometry

In this paper a new technique is presented that extracts the geometry of lumbar vertebral bodies from spiral CT scans. Our new multi-step segmentation approach yields highly accurate and precise measurement of the bone mineral density (BMD) in different volumes of interest which are defined relative to a local anatomical coordinate systems. The approach also enables the analysis of the geometry of the relevant vertebrae. Intra- and inter operator precision for segmentation, BMD measurement and position of the coordinate system are below 1.5% in patient data, accuracy errors are below 1.5% for BMD and below 4% for volume in phantom data. The long-term goal of the approach is to improve fracture prediction in osteoporosis.

Evaluation of Direct Haptic 4D Volume Rendering of Partially Segmented Data for Liver Puncture Simulation

This work presents an evaluation study using a force feedback evaluation framework for a novel direct needle force volume rendering concept in the context of liver puncture simulation. PTC/PTCD puncture interventions targeting the bile ducts have been selected to illustrate this concept. The haptic algorithms of the simulator system are based on (1) partially segmented patient image data and (2) a non-linear spring model effective at organ borders. The primary aim is to quantitatively evaluate force errors caused by our patient modeling approach, in comparison to haptic force output obtained from using gold-standard, completely manually-segmented data. The evaluation of the force algorithms compared to a force output from fully manually segmented gold-standard patient models, yields a low mean of 0.12 N root mean squared force error and up to 1.6 N for systematic maximum absolute errors. Force errors were evaluated on 31,222 preplanned test paths from 10 patients. Only twelve percent of the emitted forces along these paths were affected by errors. This is the first study evaluating haptic algorithms with deformable virtual patients in silico. We prove haptic rendering plausibility on a very high number of test paths. Important errors are below just noticeable differences for the hand-arm system.