Three-Dimensional Multi-Modality Registration for Orthopaedics and Cardiovascular Settings: State-of-the-Art and Clinical Applications

The multimodal and multidomain registration of medical images have gained increasing recognition in clinical practice as a powerful tool for fusing and leveraging useful information from different imaging techniques and in different medical fields such as cardiology and orthopedics. Image registration could be a challenging process, and it strongly depends on the correct tuning of registration parameters. In this paper, the robustness and accuracy of a landmarks-based approach have been presented for five cardiac multimodal image datasets. The study is based on 3D Slicer software and it is focused on the registration of a computed tomography (CT) and 3D ultrasound time-series of post-operative mitral valve repair. The accuracy of the method, as a function of the number of landmarks used, was performed by analysing root mean square error (RMSE) and fiducial registration error (FRE) metrics. The validation of the number of landmarks resulted in an optimal number of 10 landmarks. The mean RMSE and FRE values were 5.26 ± 3.17 and 2.98 ± 1.68 mm, respectively, showing comparable performances with respect to the literature. The developed registration process was also tested on a CT orthopaedic dataset to assess the possibility of reconstructing the damaged jaw portion for a pre-operative planning setting. Overall, the proposed work shows how 3D Slicer and registration by landmarks can provide a useful environment for multimodal/unimodal registration.

A novel non-segmented inverted water outline rendering method can improve the tracking of responsible blood vessels for hemifacial spasm

This study aimed to explore a novel, non-segmented based on inverted water outline, and rapid 3D rendering method for identifying the responsible blood vessels for hemifacial spasm. First, the software was developed using the free and open-source 3D Slicer to process magnetic resonance images. Outlines of the water region were extracted and rendered in a three-dimensional space. The traditional image re-slicing technique (IMRT) was used for the control group, while non-segmented inverted water outline rendering (NSIWR) was used to observe the relevant blood vessels in the root entry/exit zone (REZ) of patients with hemifacial spasm. The intraoperative exploration results were considered the gold standard for comparing the differences in identifying relevant blood vessels between the two methods. Twenty-five patients were included, and the reconstruction effect evaluation suggested that NSIWR could effectively reconstruct the responsible blood vessels of the cochlea, facial nerve, and REZ. Compared with IMRT, NSIWR effectively improved the diagnosis of the responsible blood vessels in the REZ, clarified their sources and directions, and was consistent with intraoperative results. This study introduced a novel rapid rendering method based on NSIWR, which was successfully applied for hemifacial spasm. The method enhances accuracy in identifying responsible blood vessels in the REZ without needing multi-modal techniques. It has the potential to improve surgical effectiveness and reduce exploration time in treating hemifacial spasm.

Exploring the Application of the Artificial-Intelligence-Integrated Platform 3D Slicer in Medical Imaging Education

Artificial Intelligence (AI) has revolutionized medical imaging procedures, specifically with regard to image segmentation, reconstruction, interpretation, and research. 3D Slicer, an open-source medical image analysis platform, has become a valuable tool in medical imaging education due to its integration of various AI applications. Through its open-source architecture, students can gain practical experience with diverse medical images and the latest AI technology, reinforcing their understanding of anatomy and imaging technology while fostering independent learning and clinical reasoning skills. The implementation of this platform improves instruction quality and nurtures skilled professionals who can meet the demands of clinical practice, research institutions, and technology innovation enterprises. AI algorithms' application in medical image processing have facilitated their translation from the lab to practical clinical applications and education.

Automatic cochlear multimodal 3D image segmentation and analysis using atlas-model-based method

Objectives: To propose an automated fast cochlear segmentation, length, and volume estimation method from clinical 3D multimodal images which has a potential role in the choice of cochlear implant type, surgery planning, and robotic surgeries.

Methods: Two datasets from different countries were used. These datasets include 219 clinical 3D images of cochlea from 3 modalities: CT, CBCT, and MR. The datasets include different ages, genders, and types of cochlear implants. We propose an atlas-model-based method for cochlear segmentation and measurement based on high-resolution μCT model and A-value. The method was evaluated using 3D landmarks located by two experts.

Results: The average error was 0.61 ± 0.22 mm and the average time required to process an image was 5.21 ± 0.93 seconds (P<0.001). The volume of the cochlea ranged from 73.96 mm3 to 106.97 mm3 , the cochlear length ranged from 36.69 to 45.91 mm at the lateral wall and from 29.12 to 39.05 mm at the organ of Corti.

Discussion: We propose a method that produces nine different automated measurements of the cochlea: volume of scala tympani, volume of scala vestibuli, central lengths of the two scalae, the scala tympani lateral wall length, and the organ of Corti length in addition to three measurements related to A-value.

Conclusion: This automatic cochlear image segmentation and analysis method can help clinician process multimodal cochlear images in approximately 5 seconds using a simple computer. The proposed method is publicly available for free download as an extension for 3D Slicer software.

Real-time integration between Microsoft HoloLens 2 and 3D Slicer with demonstration in pedicle screw placement planning

PURPOSE

Up to date, there has been a lack of software infrastructure to connect 3D Slicer to any augmented reality (AR) device. This work describes a novel connection approach using Microsoft HoloLens 2 and OpenIGTLink, with a demonstration in pedicle screw placement planning.

METHODS

We developed an AR application in Unity that is wirelessly rendered onto Microsoft HoloLens 2 using Holographic Remoting. Simultaneously, Unity connects to 3D Slicer using the OpenIGTLink communication protocol. Geometrical transform and image messages are transferred between both platforms in real time. Through the AR glasses, a user visualizes a patient's computed tomography overlaid onto virtual 3D models showing anatomical structures. We technically evaluated the system by measuring message transference latency between the platforms. Its functionality was assessed in pedicle screw placement planning. Six volunteers planned pedicle screws' position and orientation with the AR system and on a 2D desktop planner. We compared the placement accuracy of each screw with both methods. Finally, we administered a questionnaire to all participants to assess their experience with the AR system.

RESULTS

The latency in message exchange is sufficiently low to enable real-time communication between the platforms. The AR method was non-inferior to the 2D desktop planner, with a mean error of 2.1 ± 1.4 mm. Moreover, 98% of the screw placements performed with the AR system were successful, according to the Gertzbein-Robbins scale. The average questionnaire outcomes were 4.5/5.

CONCLUSIONS

Real-time communication between Microsoft HoloLens 2 and 3D Slicer is feasible and supports accurate planning for pedicle screw placement.

3D pollination biology using micro-computed tomography and geometric morphometrics in Theobroma cacao

Premise

Imaging technologies that capture three-dimensional (3D) variation in floral morphology at micro- and nano-resolutions are increasingly accessible. In herkogamous flowers, such as those of Theobroma cacao, structural barriers between anthers and stigmas represent bottlenecks that restrict pollinator size and access to reproductive organs. To study the unresolved pollination biology of cacao, we present a novel application of micro-computed tomography (micro-CT) using floral dimensions to quantify pollinator functional size limits.

Methods

We generated micro-CT data sets from field-collected flowers and museum specimens of potential pollinators. To compare floral variation, we used 3D Slicer to place landmarks on the surface models and performed a geometric morphometric (GMM) analysis using geomorph R. We identified the petal side door (an opening between the petal hoods and filament) as the main bottleneck for pollinator access. We compared its mean dimensions with proposed pollinators to identify viable candidates.

Results

We identified three levels of likelihood for putative pollinators based on the number of morphological (body) dimensions that fit through the petal side door. We also found floral reward microstructures whose presence and location were previously unclear.

Discussion

Using micro-CT and GMM to study the 3D pollination biology of cacao provides new evidence for predicting unknown pollinators. Incorporating geometry and floral rewards will strengthen plant-pollinator trait matching models for cacao and other species.

The Consistency Between the Preoperative 3D-Reconstructed Meckel's Cave and the Intraoperative Balloon Results in Percutaneous Balloon Compression

Objective

To predict the volume and shape of the balloon before PBC by reconstructing the Meckel's cave (MC) and establishing a volumetric measurement model, supporting preoperative preparation and intraoperative decisions.

Methods

The clinical data of 31 patients with good therapeutic effects who underwent PBC are retrospectively collected, including preoperative MRI, the volume of contrast agent injected into the balloon, and intraoperative lateral X-ray images. The MC on the affected side of the 31 patients is reconstructed based on MRI using 3D Slicer, while the volume of the MC is calculated to compare with the volume of contrast agent. The width (W) and length (L) of the model of the MC in lateral view are measured and used to classify the shape of the MC based on W/L. The consistency between the W/L of the model of the MC and the W/L of the intraoperative balloon is evaluated.

Results

For volume, the mean value of the models of the MC (V1) in 31 patients is 399.77±155.13 mm³, while the mean value of the contrast agent injected during PBC (V2) is 539.03±111.93 mm³. The formula obtained by linear regression is V2= 392.1 + 0.3676×V1. Based on the value of W/L, the shape of the MC is classified into thin "pear" in 5 patients (16.13%), standard "pear" in 22 patients (70.97%), and square "pear" in 4 patients (12.90%). There is no significant difference in W/L between the models of the MC and the intraoperative balloons in 31 patients (P=0.221).

Conclusion

In 31 patients with good efficacy, it is verified that the prediction of the MC before PBC by 3D Slicer is consistent with the actual situation of the intraoperative balloon. This method can provide certain basis for preoperative preparation and intraoperative judgment.

Perihematomal edema after minimally invasive surgery: a matter of concern to neurosurgeons

The purpose of this study is to explore the evolution of brain edema after minimally invasive surgery in deep spontaneous cerebral hemorrhage (DSICH) treatment and to analyze the differences in edema after different surgical methods. The clinical data of 105 patients with DSICH treated at Renmin Hospital of Wuhan University from January 2020 to June 2022 were analyzed retrospectively. Among them, 54 patients were treated with minimally invasive puncture and drainage surgery (MIPDS group), and 51 were treated with neuroendoscopic surgery (NES group). Continuous computed tomography images of patients in the hospital and 3D Slicer software were used to quantitatively calculate the edematous area to explore the changes in perihematomal edema volume in the two groups after the operation. The peak volume of postoperative edema (37.36±10.51 mL) in the MIPDS group was more extensive than that in the NES group, and its net increase in edema volume was 16.86±10.01 mL more than that in the NES group. The relative edema index (0.86±0.26) was lower in the NES group than in the MIPDS group (P < 0.05). The peak of postoperative edema in the MIPDS group was at 6-8 days after the operation, and that in the NES group was most often at 3-5 days after the operation. There are differences in perihematomal edema of DSICH treated by different minimally invasive methods. Compared with the MIPDS group, the NES group showed earlier peak of cerebral edema and lower degree of cerebral edema. The absolute regression volume of edema in the MIDPs group was greater than that in the NEs group, but there was no difference in the regression rate of edema between the two groups.

Post-operative rebleeding in patients with spontaneous supratentorial intracerebral hemorrhage: factors and clinical outcomes

OBJECTIVE

To explore factors affecting postoperative rebleeding in patients with spontaneous supratentorial intracerebral hemorrhage (SSICH).

METHODS

We retrospectively analyzed data from 724 patients with SSICH treated at Renmin Hospital of Wuhan University from December 2018 to October 2021. Finally, 294 people were eligible to be included in this study. Hematoma locations were classified as basal ganglia, thalamus, subcortex, or intraventricular. Surgery was categorized as neuroendoscopic surgery, burr hole (stereotactic drilling and drainage), or open craniotomy. Postoperative rebleeding was recorded. The incidence, risk factors, and prognosis of postoperative rebleeding were evaluated.

RESULTS

All procedures were successfully completed. Postoperative rebleeding occurred in 57 patients (19.83%, 57/294). Univariate logistic regression analysis identified these risk factors for rebleeding: admission Glasgow Coma Scale (GCS) score, irregular hematoma morphology by preoperative Computed Tomography (CT), postoperative hypertension, hematoma location, surgical method (P<0.05), and preoperative hematoma volume (P<0.1). Multivariate logistic regression analysis confirmed admission GCS score, irregular hematoma morphology by preoperative CT, postoperative hypertension, hematoma location, and surgical method as significant risk factors (P<0.05). Burr hole surgery and basal ganglia hematomas were associated with increased odds of rebleeding, and the mortality rates in patients with rebleeding versus no rebleeding were 7.02% versus 0.84%.

CONCLUSIONS

Neuroendoscopic surgery, craniotomy, and burr hole are all effective for treating SSICH, but burr hole surgery was an important risk factor for rebleeding and an adverse outcome. Admission GCS score, irregular hematoma morphology, blood pressure control, hematoma location, and surgical method are affected the risk of postoperative rebleeding. 3D Slicer-assisted neuroendoscopic surgery may be the most effective treatment for many patients with SSICH.

Three-Dimensional Volume Rendering of Pelvic Floor Anatomy with Focus on Fibroids in Relation to the Lower Urogenital Tract Based on Cross-Sectional MRI Images

We aimed to assess the feasibility of developing three-dimensional (3D) models of pelvic organs using cross-sectional MRI images of patients with uterine fibroids and urinary symptoms and of obtaining anatomical information unavailable in 2D imaging modalities. We also aimed to compare two image processing applications. We performed a feasibility study analysing MRI scans from three women, aged 30 to 58 years old, with fibroids and urinary symptoms. Cross-sectional images were used to render 3D models of pelvic anatomy, including bladder, uterus and fibroids, using 3D Slicer and OsiriX. Dimensions, volumes and anatomical relationships of the pelvic organs were evaluated. Comparisons between anatomical landmarks and measurements obtained from the two image processing applications were undertaken. Rendered 3D pelvic models yielded detailed anatomical information and data on spatial relationships that were unobtainable from cross-sectional images. Models were rendered in sufficient resolution to aid understanding of spatial relationships between urinary bladder, uterus and fibroid(s). Measurements of fibroid volumes ranged from 5,336 to 418,012 mm3 and distances between the fibroid and urinary bladder ranged from 0.10 to 83.60 mm. Statistical analysis of measurements showed no significant differences in measurements between the two image processing applications. To date, limited data exist on the use of 3D volume reconstructions of routine MRI scans, to investigate pelvic pathologies such as fibroids in women with urinary symptoms. This study suggests that post-MRI image processing can provide additional information over standard MRI. Further studies are required to assess the role of these data in clinical practice, surgical planning and training. Three-dimensional reconstruction of routine two-dimensional magnetic resonance imaging provides additional anatomical information and may improve our understanding of anatomical relationships, their role in clinical presentations and possibly guide clinical and surgical management.

Volume of Aneurysmal Subarachnoid Hematoma Measured Quantitatively by 3D Slicer to Predict Symptomatic Cerebral Vasospasm

Background and Objectives

Aneurysmal subarachnoid hemorrhage is strongly associated with symptomatic cerebral vasospasm. This study aims to investigate whether a quantitative measure of aneurysmal subarachnoid hematoma by 3D Slicer is more valuable for vasospasm risk prediction compared with modified Fisher scale and the new scale by Eagles.

Materials and Methods

We performed a retrospective research of Digital Imaging and Communications in Medicine format (DICOM) in aneurysmal patients treated at our institution from 2019 to 2020. Association between vasospasm and hematoma volume by 3D Slicer was explored by univariate and multivariate analyses. Value of risk prediction was compared through area under the receiver operator characteristic curve (AUC) among the modified Fisher scale, the new scale by Eagles, and hematoma volume by 3D Slicer.

Results

Hematoma volume by 3D Slicer had a significant relationship with vasospasm both by one-way analysis of variance (ANOVA; F = 19.37, P < 0.001) and a binary logistic regression analysis (odds ratio [OR] = 1.05, P = 0.016). Hematoma volume by 3D Slicer had a significantly higher AUC (0.708; 95% confidence interval [CI]: 0.618-0.798, P < 0.001) than the modified Fisher scale and the new scale by Eagles. The optimal diagnostic threshold for hematoma volume by 3D Slicer was 15.98 ml, and the sensitivity and specificity were 73.5% and 58.6%, respectively.

Conclusions

Volume of aneurysmal subarachnoid hematoma measured quantitatively by 3D Slicer can improve the predictive value for symptomatic cerebral vasospasm.

Advantages of a Training Course for Surgical Planning in Virtual Reality for Oral and Maxillofacial Surgery: Crossover Study

BACKGROUND

As an integral part of computer-assisted surgery, virtual surgical planning (VSP) leads to significantly better surgery results, such as for oral and maxillofacial reconstruction with microvascular grafts of the fibula or iliac crest. It is performed on a 2D computer desktop screen (DS) based on preoperative medical imaging. However, in this environment, VSP is associated with shortcomings, such as a time-consuming planning process and the requirement of a learning process. Therefore, a virtual reality (VR)-based VSP application has great potential to reduce or even overcome these shortcomings due to the benefits of visuospatial vision, bimanual interaction, and full immersion. However, the efficacy of such a VR environment has not yet been investigated.

OBJECTIVE

This study aimed to demonstrate the possible advantages of a VR environment through a substep of VSP, specifically the segmentation of the fibula (calf bone) and os coxae (hip bone), by conducting a training course in both DS and VR environments and comparing the results.

METHODS

During the training course, 6 novices were taught how to use a software application in a DS environment (3D Slicer) and in a VR environment (Elucis) for the segmentation of the fibula and os coxae, and they were asked to carry out the maneuvers as accurately and quickly as possible. Overall, 13 fibula and 13 os coxae were segmented for each participant in both methods (VR and DS), resulting in 156 different models (78 fibula and 78 os coxae) per method (VR and DS) and 312 models in total. The individual learning processes in both environments were compared using objective criteria (time and segmentation performance) and self-reported questionnaires. The models resulting from the segmentation were compared mathematically (Hausdorff distance and Dice coefficient) and evaluated by 2 experienced radiologists in a blinded manner.

RESULTS

A much faster learning curve was observed for the VR environment than the DS environment (β=.86 vs β=.25). This nearly doubled the segmentation speed (cm³/min) by the end of training, leading to a shorter time (P<.001) to reach a qualitative result. However, there was no qualitative difference between the models for VR and DS (P=.99). The VR environment was perceived by participants as more intuitive and less exhausting, and was favored over the DS environment.

CONCLUSIONS

The more rapid learning process and the ability to work faster in the VR environment could save time and reduce the VSP workload, providing certain advantages over the DS environment.

Utilizing 3D Slicer to incorporate tomographic images into GATE Monte Carlo simulation for personalized dosimetry in yttrium-90 radioembolization

PURPOSE

Monte Carlo (MC) simulation is an important technique that can help design advanced and challenging experimental setups. GATE (Geant4 application for tomographic emission) is a useful simulation toolkit for applications in nuclear medicine. Transarterial radioembolization is a treatment for liver cancer, where microspheres embedded with yttrium-90 (⁹⁰ Y) are administered intra-arterially to the tumor. Personalized dosimetry for this treatment may provide higher dosimetry accuracy compared to the conventional partition model (PM) calculation. However, incorporation of three-dimensional tomographic input data into MC simulation is an intricate process. In this article, 3D Slicer, free and open-source software, was utilized for the incorporation of patient tomographic images into GATE to demonstrate the feasibility of personalized dosimetry in hepatic radioembolization with ⁹⁰ Y.

METHODS

In this article, the steps involved in importing, segmenting, and registering tomographic images using 3D Slicer were thoroughly described, before importing them into GATE for MC simulation. The absorbed doses estimated using GATE were then compared with that of PM. SlicerRT, a 3D Slicer extension, was then used to visualize the isodose from the MC simulation.

RESULTS

A workflow diagram consisting of all the steps taken in the utilization of 3D Slicer for personalized dosimetry in ⁹⁰ Y radioembolization has been presented in this article. In comparison to the MC simulation, the absorbed doses to the tumor and normal liver were overestimated by PM by 105.55% and 20.23%, respectively, whereas for lungs, the absorbed dose estimated by PM was underestimated by 25.32%. These values were supported by the isodose distribution obtained via SlicerRT, suggesting the presence of beta particles outside the volumes of interest. These findings demonstrate the importance of personalized dosimetry for a more accurate absorbed dose estimation compared to PM.

CONCLUSION

The methodology provided in this study can assist users (especially students or researchers who are new to MC simulation) in navigating intricate steps required in the importation of tomographic data for MC simulation. These steps can also be utilized for other radiation therapy related applications, not necessarily limited to internal dosimetry.

Bridging 3D Slicer and ROS2 for Image-Guided Robotic Interventions

Developing image-guided robotic systems requires access to flexible, open-source software. For image guidance, the open-source medical imaging platform 3D Slicer is one of the most adopted tools that can be used for research and prototyping. Similarly, for robotics, the open-source middleware suite robot operating system (ROS) is the standard development framework. In the past, there have been several "ad hoc" attempts made to bridge both tools; however, they are all reliant on middleware and custom interfaces. Additionally, none of these attempts have been successful in bridging access to the full suite of tools provided by ROS or 3D Slicer. Therefore, in this paper, we present the SlicerROS2 module, which was designed for the direct use of ROS2 packages and libraries within 3D Slicer. The module was developed to enable real-time visualization of robots, accommodate different robot configurations, and facilitate data transfer in both directions (between ROS and Slicer). We demonstrate the system on multiple robots with different configurations, evaluate the system performance and discuss an image-guided robotic intervention that can be prototyped with this module. This module can serve as a starting point for clinical system development that reduces the need for custom interfaces and time-intensive platform setup.

A new method of preoperative assessment of correct electrode array alignment based on post-operative measurements in a cochlear implanted cohort

PURPOSE

During cochlear implantation surgery, a range of complications may occur such as tip fold-over. We recently developed a method to estimate the insertion orientation of the electrode array. The aim of the study was to determine the optimal angle of orientation in a cohort of cochlear implanted patients.

METHODS

On eighty-five CT scans (80 uncomplicated insertions and 5 cases with tip fold-over), location of the electrode array's Insertion Guide (IG), Orientation marker (OM) and two easily identifiable landmarks (the round window (RW) and the incus short process (ISP)) were manually marked. The angle enclosed by ISP-RW line and the Cochlear™ Slim Modiolar electrode array's OM line determined the electrode array insertion angle.

RESULTS

The average insertion angle was 45.0-47.2° ± 10.4-12° SD and was validated with 98% confidence interval. Based on the measurements obtained, patients' sex and age had no impact on the size of this angle. Although the angles of the tip fold-over cases (44.9°, 46.9°, 34.2°, 54.3°, 55.9°) fell within this average range, the further it diverted from the average it increased the likelihood for tip fold-over.

CONCLUSION

Electrode array insertion in the individually calculated angle relative to the visible incus short process provides a useful guide for the surgeon when aiming for the optimal angle, and potentially enhances good surgical outcomes. Our results show that factors other than the orientation angle may additionally contribute to failures in implantation when the Slim Modiolar electrode is used.

Semi-Automatic Segmentation of Cone Beam Computed Tomography Datasets for Volume Measurements of Equine Cheek Teeth

The volumes of equine teeth may change considerably over time for several reasons including domestication, routine dental floating, and the hypsodont and anelodont nature of the teeth. Cone beam computed tomography (CBCT) of the head is routinely performed in standing horses and, in this proof of concept study, the feasibility of measuring tooth volume from CBCT datasets was determined. The CBCT images of 5 equine cadaver cheek teeth were segmented with a software 3-dimensional (3D) Slicer using a predefined protocol, corrected manually, and re-assembled into a 3D model. Individual tooth volume (V_S) was calculated from the model. After extraction, the volumes were also measured using the "gold-standard" water displacement method (V_W) for comparison. The V_S of 77 teeth ranged from 7114 to 42,300 mm³ which strongly correlated with V_W (r = 0.99)_, and on average V_S was 6.1% less than V_W. There was no significant difference in V_S between the right and left arcades in individual animals. Maxillary cheek tooth volume was on average 40% larger than it was for mandibular counterparts. Semi-automatic image segmentation of equine cheek teeth from CBCT data is feasible and accurate but requires some manual intervention. This preliminary study provides initial data on the volume of equine cheek teeth and creates new possibilities for future in vivo studies.

Choroidal macrovessel: Systematic review and analysis of anatomic origin

There are various hypotheses for the anatomic origin of a choroidal macrovessel. We assess whether a choroidal macrovessel is a dilated posterior ciliary artery. A systematic review of published literature on choroidal macrovessels was performed with two additional cases from our institution. We compared the visible entry and vascular course of the macrovessel in the published literature. We performed a comparative analysis using indocyanine green angiography, swept source optical computed tomography, and 3D reconstruction of two choroidal macrovessels using 3D Slicer (Harvard, Boston, USA, https://www.slicer.org/). From the 14 studies found, 18 cases met inclusion criteria. The reported literature and our two cases showed a radiating course along a sectoral distribution pattern of either short or long posterior ciliary arteries. Our review of literature and 3D reconstruction analysis support the hypothesis that choroidal macrovessels are dilated posterior ciliary arteries.

SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller

Interaction between medical image platform and external environment is a desirable feature in several clinical, research, and educational scenarios. In this work, the integration between 3D Slicer package and Arduino board is introduced, enabling a simple and useful communication between the two software/hardware platforms. The open source extension, programmed in Python language, manages the connection process and offers a communication layer accessible from any point of the medical image suite infrastructure. Deep integration with 3D Slicer code environment is provided and a basic input–output mechanism accessible via GUI is also made available. To test the proposed extension, two exemplary use cases were implemented: (1) INPUT data to 3D Slicer, to navigate on basis of data detected by a distance sensor connected to the board, and (2) OUTPUT data from 3D Slicer, to control a servomotor on the basis of data computed through image process procedures. Both goals were achieved and quasi-real-time control was obtained without any lag or freeze, thus boosting the integration between 3D Slicer and Arduino. This integration can be easily obtained through the execution of few lines of Python code. In conclusion, SlicerArduino proved to be suitable for fast prototyping, basic input–output interaction, and educational purposes. The extension is not intended for mission-critical clinical tasks.

Development and evaluation of a "trackerless" surgical planning and guidance system based on 3D Slicer

Conventional optical tracking systems use cameras sensitive to near-infrared (NIR) light and NIR illuminated/active-illuminating markers to localize instrumentation and the patient in the operating room (OR) physical space. This technology is widely used within the neurosurgical theater and is a staple in the standard of care for craniotomy planning. To accomplish, planning is largely conducted at the time of the procedure in the OR with the patient in a fixed head orientation. We propose a framework to achieve this in the OR without conventional tracking technology, i.e., a "trackerless" approach. Briefly, we investigate an extension of the 3D Slicer which combines surgical planning and craniotomy designation. While taking advantage of the well-developed 3D Slicer platform, we implement advanced features to aid the neurosurgeon in planning the location of the anticipated craniotomy relative to the preoperatively imaged tumor in a physical-to-virtual setup, and then subsequently aid the true physical procedure by correlating that physical-to-virtual plan with an intraoperative magnetic resonance imaging-to-physical registered field-of-view display. These steps are done such that the craniotomy can be designated without the use of a conventional optical tracking technology. To test this approach, four experienced neurosurgeons performed experiments on five different surgical cases using our 3D Slicer module as well as the conventional procedure for comparison. The results suggest that our planning system provides a simple, cost-efficient, and reliable solution for surgical planning and delivery without the use of conventional tracking technologies. We hypothesize that the combination of this craniotomy planning approach and our past developments in cortical surface registration and deformation tracking using stereo-pair data from the surgical microscope may provide a fundamental realization of an integrated trackerless surgical guidance platform.

New, simple and reliable volumetric calculation technique in incisional hernias with loss of domain

INTRODUCTION

The management of hernias with loss of domain is a challenging problem. It has been shown that the volume of the incisional hernia/peritoneal volume ratio < 20% was a predictive factor for tension-free fascia closure, after pre-operative pneumoperitoneum preparation (Goni Moreno technique). In this study, we propose an easy, reliable and fast technique to perform volumetric calculation, by the surgeon alone.

MATERIALS AND METHODS

3D slicer software (free open-source software) was used to calculate with precision the intra-peritoneal and intra-hernia volumes, and to create a 3D reconstruction of both volumes. The measurement technique is described step by step using detailed figures and videos.

RESULTS

The method was used to calculate the volumes for five consecutive patients, managed between January 2018 and March 2019. All the five patients had a ratio greater than 20% and, therefore, received a PPP program. The effectiveness of the procedure is objectified by the increase of the intraabdominal volume and the reduction of the incisional hernia/peritoneal volume ratio. The feasibility of a tension-free fascia closure was confirmed for the five patients.

CONCLUSION

In addition to a standardized definition of "loss of domain", a standardized volumetric technique, easy to reproduce, needs to be adopted. Our method can be done by any surgeon with basic computer skills and radiological knowledge in an autonomous and a fast manner, thus helping to select the right technique for the right patient.

Intracranial Mirror Aneurysm: Epidemiology, Rupture Risk, New Imaging, Controversies, and Treatment Strategies

There are some controversies about the surgical treatment strategy of mirror aneurysms. Whether to choose 1-stage or 2-stage surgery, bilateral or unilateral craniotomy, or surgical or interventional treatment are the main points in dispute. In this review, the different surgery strategies faced by patients are discussed. Different surgical methods are adopted based on the patient's individual state and the location and size of the aneurysm. A new imaging method is introduced using 3D Slicer, which clearly recognizes the relationship among aneurysm, brain tissue, skull, and nerve. The 3D Slicer can help surgeons undertake adequate preoperative preparation. In addition, we also introduce some ruptured factors (e.g., age, gender, hypertension, morphologic, and hemodynamic) concerning mirror aneurysm. Systematic discussion of the controversies and methods in surgical treatment of mirror aneurysms may provide new perspectives in future research for the prevention and treatment of mirror aneurysms.

Polymorph segmentation representation for medical image computing

BACKGROUND AND OBJECTIVE

Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects.

METHODS

A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in the Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions.

RESULTS

The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications.

CONCLUSIONS

A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software's BSD-style open-source license allows complete freedom of use of the library.

A wearable mixed-reality holographic computer for guiding external ventricular drain insertion at the bedside

OBJECTIVE

The goal of this study was to explore the feasibility and accuracy of using a wearable mixed-reality holographic computer to guide external ventricular drain (EVD) insertion and thus improve on the accuracy of the classic freehand insertion method for EVD insertion. The authors also sought to provide a clinically applicable workflow demonstration.

METHODS

Pre- and postoperative CT scanning were performed routinely by the authors for every patient who needed EVD insertion. Hologram-guided EVD placement was prospectively applied in 15 patients between August and November 2017. During surgical planning, model reconstruction and trajectory calculation for each patient were completed using preoperative CT. By wearing a Microsoft HoloLens, the neurosurgeon was able to visualize the preoperative CT-generated holograms of the surgical plan and perform EVD placement by keeping the catheter aligned with the holographic trajectory. Fifteen patients who had undergone classic freehand EVD insertion were retrospectively included as controls. The feasibility and accuracy of the hologram-guided technique were evaluated by comparing the time required, number of passes, and target deviation for hologram-guided EVD placement with those for classic freehand EVD insertion.

RESULTS

Surgical planning and hologram visualization were performed in all 15 cases in which EVD insertion involved holographic guidance. No adverse events related to the hologram-guided procedures were observed. The mean ± SD additional time before the surgical part of the procedure began was 40.20 ± 10.74 minutes. The average number of passes was 1.07 ± 0.258 in the holographic guidance group, compared with 2.33 ± 0.98 in the control group (p < 0.01). The mean target deviation was 4.34 ± 1.63 mm in the holographic guidance group and 11.26 ± 4.83 mm in the control group (p < 0.01).

CONCLUSIONS

This study demonstrates the use of a head-mounted mixed-reality holographic computer to successfully perform hologram-assisted bedside EVD insertion. A full set of clinically applicable workflow images is presented to show how medical imaging data can be used by the neurosurgeon to visualize patient-specific holograms that can intuitively guide hands-on operation. The authors also provide preliminary confirmation of the feasibility and accuracy of this hologram-guided EVD insertion technique.

Osteotomy Planner: An open-source tool for osteotomy simulation

There has been a recent emphasis in surgical science on supplementing surgical training outside of the Operating Room (OR). Combining simulation training with the current surgical apprenticeship enhances surgical skills in the OR, without increasing the time spent in the OR practicing. Computer-assisted surgical (CAS) planning consists of performing operative techniques virtually using three-dimensional (3D) computer-based models reconstructed from 3D cross-sectional imaging. The purpose of this paper is to present a CAS system to rehearse, visualize and quantify osteotomies, and demonstrate its usefulness in two different osteotomy surgical procedures, cranial vault reconstruction and femoral osteotomy. We found that the system could sufficiently simulate these two procedures. Our system takes advantage of the high-quality visualizations possible with 3DSlicer, as well as implements new infrastructure to allow for direct 3D interaction (cutting and positioning) with the bone models. We see the proposed osteotomy planner tool evolving towards incorporating different cutting templates to help depict several surgical scenarios, help 'trained' surgeons maintain operating skills, help rehearse a surgical sequence before heading to the OR, or even to help surgical planning for specific patient cases.

A new device for fiducial registration of image-guided navigation system for liver RFA

PURPOSE

Radiofrequency ablation for liver tumors (liver RFA) is widely performed under ultrasound guidance. However, discriminating between the tumor and the needle is often difficult because of cavitation caused by RFA-induced coagulation. An unclear ultrasound image can lead to complications and tumor residue. Therefore, image-guided navigation systems based on fiducial registration have been developed. Fiducial points are usually set on a patient's skin. But the use of internal fiducial points can improve the accuracy of navigation. In this study, a new device is introduced to use internal fiducial points using 2D US.

METHODS

3D Slicer as the navigation software, Polaris Vicra as the position sensor, and two target tumors in a 3D abdominal phantom as puncture targets were used. Also, a new device that makes it possible to obtain tracking coordinates in the body was invented. First, two-dimensional reslice images from the CT images using 3D Slicer were built. A virtual needle was displayed on the two-dimensional reslice image, reflecting the movement of the actual needle after fiducial registration. A phantom experiment using three sets of fiducial point configurations: one conventional case using only surface points, and two cases in which the center of the target tumor was selected as a fiducial point was performed. For each configuration, one surgeon punctured each target tumor ten times under guidance from the 3D Slicer display. Finally, a statistical analysis examining the puncture error was performed.

RESULTS

The puncture error for each target tumor decreased significantly when the center of the target tumor was included as one of the fiducial points, compared with when only surface points were used.

CONCLUSION

This study introduces a new device to use internal fiducial points and suggests that the accuracy of image-guided navigation systems for liver RFA can be improved by using the new device.

Development of a surgical navigation system based on 3D Slicer for intraoperative implant placement surgery

Implant placement has been widely used in various kinds of surgery. However, accurate intraoperative drilling performance is essential to avoid injury to adjacent structures. Although some commercially-available surgical navigation systems have been approved for clinical applications, these systems are expensive and the source code is not available to researchers. 3D Slicer is a free, open source software platform for the research community of computer-aided surgery. In this study, a loadable module based on Slicer has been developed and validated to support surgical navigation. This research module allows reliable calibration of the surgical drill, point-based registration and surface matching registration, so that the position and orientation of the surgical drill can be tracked and displayed on the computer screen in real time, aiming at reducing risks. In accuracy verification experiments, the mean target registration error (TRE) for point-based and surface-based registration were 0.31±0.06mm and 1.01±0.06mm respectively, which should meet clinical requirements. Both phantom and cadaver experiments demonstrated the feasibility of our surgical navigation software module.

Assessing the Effects of Software Platforms on Volumetric Segmentation of Glioblastoma

Background

Radiological assessments of biologically relevant regions in glioblastoma have been associated with genotypic characteristics, implying a potential role in personalized medicine. Here, we assess the reproducibility and association with survival of two volumetric segmentation platforms and explore how methodology could impact subsequent interpretation and analysis.

Methods

Post-contrast T1- and T2-weighted FLAIR MR images of 67 TCGA patients were segmented into five distinct compartments (necrosis, contrast-enhancement, FLAIR, post contrast abnormal, and total abnormal tumor volumes) by two quantitative image segmentation platforms - 3D Slicer and a method based on Velocity AI and FSL. We investigated the internal consistency of each platform by correlation statistics, association with survival, and concordance with consensus neuroradiologist ratings using ordinal logistic regression.

Results

We found high correlations between the two platforms for FLAIR, post contrast abnormal, and total abnormal tumor volumes (spearman’s r(67) = 0.952, 0.959, and 0.969 respectively). Only modest agreement was observed for necrosis and contrast-enhancement volumes (r(67) = 0.693 and 0.773 respectively), likely arising from differences in manual and automated segmentation methods of these regions by 3D Slicer and Velocity AI/FSL, respectively. Survival analysis based on AUC revealed significant predictive power of both platforms for the following volumes: contrast-enhancement, post contrast abnormal, and total abnormal tumor volumes. Finally, ordinal logistic regression demonstrated correspondence to manual ratings for several features.

Conclusion

Tumor volume measurements from both volumetric platforms produced highly concordant and reproducible estimates across platforms for general features. As automated or semi-automated volumetric measurements replace manual linear or area measurements, it will become increasingly important to keep in mind that measurement differences between segmentation platforms for more detailed features could influence downstream survival or radio genomic analyses.

Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

Pre-clinical validation of virtual bronchoscopy using 3D Slicer

PURPOSE

Lung cancer still represents the leading cause of cancer-related death, and the long-term survival rate remains low. Computed tomography (CT) is currently the most common imaging modality for lung diseases recognition. The purpose of this work was to develop a simple and easily accessible virtual bronchoscopy system to be coupled with a customized electromagnetic (EM) tracking system for navigation in the lung and which requires as little user interaction as possible, while maintaining high usability.

METHODS

The proposed method has been implemented as an extension to the open-source platform, 3D Slicer. It creates a virtual reconstruction of the airways starting from CT images for virtual navigation. It provides tools for pre-procedural planning and virtual navigation, and it has been optimized for use in combination with a [Formula: see text] of freedom EM tracking sensor. Performance of the algorithm has been evaluated in ex vivo and in vivo testing.

RESULTS

During ex vivo testing, nine volunteer physicians tested the implemented algorithm to navigate three separate targets placed inside a breathing pig lung model. In general, the system proved easy to use and accurate in replicating the clinical setting and seemed to help choose the correct path without any previous experience or image analysis. Two separate animal studies confirmed technical feasibility and usability of the system.

CONCLUSIONS

This work describes an easily accessible virtual bronchoscopy system for navigation in the lung. The system provides the user with a complete set of tools that facilitate navigation towards user-selected regions of interest. Results from ex vivo and in vivo studies showed that the system opens the way for potential future work with virtual navigation for safe and reliable airway disease diagnosis.

Morphological and Volumetric Assessment of Cerebral Ventricular System with 3D Slicer Software

We present a technological process based on the 3D Slicer software for the three-dimensional study of the brain's ventricular system with teaching purposes. It values the morphology of this complex brain structure, as a whole and in any spatial position, being able to compare it with pathological studies, where its anatomy visibly changes. 3D Slicer was also used to obtain volumetric measurements in order to provide a more comprehensive and detail representation of the ventricular system. We assess the potential this software has for processing high resolution images, taken from Magnetic Resonance and generate the three-dimensional reconstruction of ventricular system.

Three-dimensional Printing and 3D Slicer: Powerful Tools in Understanding and Treating Structural Lung Disease

Recent advances in the three-dimensional (3D) printing industry have enabled clinicians to explore the use of 3D printing in preprocedural planning, biomedical tissue modeling, and direct implantable device manufacturing. Despite the increased adoption of rapid prototyping and additive manufacturing techniques in the health-care field, many physicians lack the technical skill set to use this exciting and useful technology. Additionally, the growth in the 3D printing sector brings an ever-increasing number of 3D printers and printable materials. Therefore, it is important for clinicians to keep abreast of this rapidly developing field in order to benefit. In this Ahead of the Curve, we review the history of 3D printing from its inception to the most recent biomedical applications. Additionally, we will address some of the major barriers to wider adoption of the technology in the medical field. Finally, we will provide an initial guide to 3D modeling and printing by demonstrating how to design a personalized airway prosthesis via 3D Slicer. We hope this information will reduce the barriers to use and increase clinician participation in the 3D printing health-care sector.

Low-Cost Interactive Image-Based Virtual Endoscopy for the Diagnosis and Surgical Planning of Suprasellar Arachnoid Cysts

OBJECTIVE

To investigate the feasibility and reliability of virtual endoscopy (VE) as a rapid, low-cost, and interactive tool for the diagnosis and surgical planning of suprasellar arachnoid cysts (SACs).

METHODS

Eighteen patients with SACs treated with endoscopic ventriculocystostomy were recruited, and 18 endoscopic patients treated with third ventriculostomy were randomly selected as a VE reconstruction control group. After loading their DICOM data into free 3D Slicer software, VE reconstruction was independently performed by 3 blinded clinicians and the time required for each reconstruction was recorded. Another 3 blinded senior neurosurgeons interactively graded the visibility of VE by watching video recordings of the endoscopic procedures. Based on the visibility scores, receiver operating characteristic curve analysis was used to investigate the reliability of VE to diagnose SACs, and Bland-Altman plots were used to assess the reliability of VE for surgical planning. In addition, the intraclass correlation coefficient was calculated to estimate the consistency among the results of 3 reconstruction performers.

RESULTS

All 3 independent reconstructing performers successfully completed VE simulation for all cases, and the average reconstruction time was 10.2 ± 9.7 minutes. The area under the receiver operating characteristic curve of the cyst visibility score was 0.96, implying its diagnostic value for SACs. The Bland-Altman plot indicated good agreement between VE and intraoperative viewings, suggesting the anatomic accuracy of the VE for surgical planning. In addition, the intraclass correlation coefficient was 0.81, which revealed excellent interperformer consistency of our simulation method.

CONCLUSIONS

This study substantiated the feasibility and reliability of VE as a rapid, low-cost, and interactive modality for diagnosis and surgical planning of SACs.

Live ultrasound volume reconstruction using scout scanning

INTRODUCTION

Ultrasound-guided interventions often necessitate scanning of deep-seated anatomical structures that may be hard to visualize. Visualization can be improved using reconstructed 3D ultrasound volumes. High-resolution 3D reconstruction of a large area during clinical interventions is challenging if the region of interest is unknown. We propose a two-stage scanning method allowing the user to perform quick low-resolution scouting followed by high-resolution live volume reconstruction.

METHODS

Scout scanning is accomplished by stacking 2D tracked ultrasound images into a low-resolution volume. Then, within a region of interest defined in the scout scan, live volume reconstruction can be performed by continuous scanning until sufficient image density is achieved. We implemented the workflow as a module of the open-source 3D Slicer application, within the SlicerIGT extension and building on the PLUS toolkit.

RESULTS

Scout scanning is performed in a few seconds using 3 mm spacing to allow region of interest definition. Live reconstruction parameters are set to provide good image quality (0.5 mm spacing, hole filling enabled) and feedback is given during live scanning by regularly updated display of the reconstructed volume.

DISCUSSION

Use of scout scanning may allow the physician to identify anatomical structures. Subsequent live volume reconstruction in a region of interest may assist in procedures such as targeting needle interventions or estimating brain shift during surgery.