Automatic liver segmentation and assessment of liver fibrosis using deep learning with MR T1-weighted images in rats

OBJECTIVES

To validate the performance of nnU-Net in segmentation and CNN in classification for liver fibrosis using T1-weighted images.

MATERIALS AND METHODS

In this prospective study, animal models of liver fibrosis were induced by injecting subcutaneously a mixture of Carbon tetrachloride and olive oil. A total of 99 male Wistar rats were successfully induced and underwent MR scanning with no contrast agent to get T1-weighted images. The regions of interest (ROIs) of the whole liver were delineated layer by layer along the liver edge by 3D Slicer. For segmentation task, all T1-weighted images were randomly divided into training and test cohorts in a ratio of 7:3. For classification, images containing the hepatic maximum diameter of every rat were selected and 80% images of no liver fibrosis (NLF), early liver fibrosis (ELF) and progressive liver fibrosis (PLF) stages were randomly selected for training, while the rest were used for testing. Liver segmentation was performed by the nnU-Net model. The convolutional neural network (CNN) was used for classification task of liver fibrosis stages. The Dice similarity coefficient was used to evaluate the segmentation performance of nnU-Net. Confusion matrix, ROC curve and accuracy were used to show the classification performance of CNN.

RESULTS

A total of 2628 images were obtained from 99 Wistar rats by MR scanning. For liver segmentation by nnU-Net, the Dice similarity coefficient in the test set was 0.8477. The accuracies of CNN in staging NLF, ELF and PLF were 0.73, 0.89 and 0.84, respectively. The AUCs were 0.76, 0.88 and 0.79, respectively.

CONCLUSION

The nnU-Net architecture is of high accuracy for liver segmentation and CNN for assessment of liver fibrosis with T1-weighted images.

An open source auto-segmentation algorithm for delineating heart and substructures - Development and validation within a multicenter lung cancer cohort

BACKGROUND AND PURPOSE

Irradiation of the heart in thoracic cancers raises toxicity concerns. For accurate dose estimation, automated heart and substructure segmentation is potentially useful. In this study, a hybrid automatic segmentation is developed. The accuracy of delineation and dose predictions were evaluated, testing the method's potential within heart toxicity studies.

MATERIALS AND METHODS

The hybrid segmentation method delineated the heart, four chambers, three large vessels, and the coronary arteries. The method consisted of a nnU-net heart segmentation and partly atlas- and model-based segmentation of the substructures. The nnU-net training and atlas segmentation was based on lung cancer patients and was validated against a national consensus dataset of 12 patients with breast cancer. The accuracy of dose predictions between manual and auto-segmented heart and substructures was evaluated by transferring the dose distribution of 240 previously treated lung cancer patients to the consensus data set.

RESULTS

The hybrid auto-segmentation method performed well with a heart dice similarity coefficient (DSC) of 0.95, with no statistically significant difference between the automatic and manual delineations. The DSC for the chambers varied from 0.78-0.86 for the automatic segmentation and was comparable with the inter-observer variability. Most importantly, the automatic segmentation was as precise as the clinical experts in predicting the dose distribution to the heart and all substructures.

CONCLUSION

The hybrid segmentation method performed well in delineating the heart and substructures. The prediction of dose by the automatic segmentation was aligned with the manual delineations, enabling measurement of heart and substructure dose in large cohorts. The delineation algorithm will be available for download.

An open-source nnU-net algorithm for automatic segmentation of MRI scans in the male pelvis for adaptive radiotherapy

Background

Adaptive MRI-guided radiotherapy (MRIgRT) requires accurate and efficient segmentation of organs and targets on MRI scans. Manual segmentation is time-consuming and variable, while deformable image registration (DIR)-based contour propagation may not account for large anatomical changes. Therefore, we developed and evaluated an automatic segmentation method using the nnU-net framework.

Methods

The network was trained on 38 patients (76 scans) with localized prostate cancer and tested on 30 patients (60 scans) with localized prostate, metastatic prostate, or bladder cancer treated at a 1.5 T MRI-linac at our institution. The performance of the network was compared with the current clinical workflow based on DIR. The segmentation accuracy was evaluated using the Dice similarity coefficient (DSC), mean surface distance (MSD), and Hausdorff distance (HD) metrics.

Results

The trained network successfully segmented all 600 structures in the test set. High similarity was obtained for most structures, with 90% of the contours having a DSC above 0.9 and 86% having an MSD below 1 mm. The largest discrepancies were found in the sigmoid and colon structures. Stratified analysis on cancer type showed that the best performance was seen in the same type of patients that the model was trained on (localized prostate). Especially in patients with bladder cancer, the performance was lower for the bladder and the surrounding organs. A complete automatic delineation workflow took approximately 1 minute. Compared with contour transfer based on the clinically used DIR algorithm, the nnU-net performed statistically better across all organs, with the most significant gain in using the nnU-net seen for organs subject to more considerable volumetric changes due to variation in the filling of the rectum, bladder, bowel, and sigmoid.

Conclusion

We successfully trained and tested a network for automatically segmenting organs and targets for MRIgRT in the male pelvis region. Good test results were seen for the trained nnU-net, with test results outperforming the current clinical practice using DIR-based contour propagation at the 1.5 T MRI-linac. The trained network is sufficiently fast and accurate for clinical use in an online setting for MRIgRT. The model is provided as open-source.

A vendor-agnostic, PACS integrated, and DICOM-compatible software-server pipeline for testing segmentation algorithms within the clinical radiology workflow

Background

Reproducible approaches are needed to bring AI/ML for medical image analysis closer to the bedside. Investigators wishing to shadow test cross-sectional medical imaging segmentation algorithms on new studies in real-time will benefit from simple tools that integrate PACS with on-premises image processing, allowing visualization of DICOM-compatible segmentation results and volumetric data at the radiology workstation.

Purpose

In this work, we develop and release a simple containerized and easily deployable pipeline for shadow testing of segmentation algorithms within the clinical workflow.

Methods

Our end-to-end automated pipeline has two major components- 1. A router/listener and anonymizer and an OHIF web viewer backstopped by a DCM4CHEE DICOM query/retrieve archive deployed in the virtual infrastructure of our secure hospital intranet, and 2. An on-premises single GPU workstation host for DICOM/NIfTI conversion steps, and image processing. DICOM images are visualized in OHIF along with their segmentation masks and associated volumetry measurements (in mL) using DICOM SEG and structured report (SR) elements. Since nnU-net has emerged as a widely-used out-of-the-box method for training segmentation models with state-of-the-art performance, feasibility of our pipleine is demonstrated by recording clock times for a traumatic pelvic hematoma nnU-net model.

Results

Mean total clock time from PACS send by user to completion of transfer to the DCM4CHEE query/retrieve archive was 5 min 32 s (± SD of 1 min 26 s). This compares favorably to the report turnaround times for whole-body CT exams, which often exceed 30 min, and illustrates feasibility in the clinical setting where quantitative results would be expected prior to report sign-off. Inference times accounted for most of the total clock time, ranging from 2 min 41 s to 8 min 27 s. All other virtual and on-premises host steps combined ranged from a minimum of 34 s to a maximum of 48 s.

Conclusion

The software worked seamlessly with an existing PACS and could be used for deployment of DL models within the radiology workflow for prospective testing on newly scanned patients. Once configured, the pipeline is executed through one command using a single shell script. The code is made publicly available through an open-source license at "https://github.com/vastc/," and includes a readme file providing pipeline config instructions for host names, series filter, other parameters, and citation instructions for this work.

A vendor-agnostic, PACS integrated, and DICOMcompatible software-server pipeline for testing segmentation algorithms within the clinical radiology workflow

Background

Reproducible approaches are needed to bring AI/ML for medical image analysis closer to the bedside. Investigators wishing to shadow test cross-sectional medical imaging segmentation algorithms on new studies in real-time will benefit from simple tools that integrate PACS with on-premises image processing, allowing visualization of DICOM-compatible segmentation results and volumetric data at the radiology workstation.

Purpose

In this work, we develop and release a simple containerized and easily deployable pipeline for shadow testing of segmentation algorithms within the clinical workflow.

Methods

Our end-to-end automated pipeline has two major components-1. a router/listener and anonymizer and an OHIF web viewer backstopped by a DCM4CHEE DICOM query/retrieve archive deployed in the virtual infrastructure of our secure hospital intranet, and 2. An on-premises single GPU workstation host for DICOM/NIfTI conversion steps, and image processing. DICOM images are visualized in OHIF along with their segmentation masks and associated volumetry measurements (in mL) using DICOM SEG and structured report (SR) elements. Feasibility is demonstrated by recording clock times for a traumatic pelvic hematoma cascaded nnU-net model.

Results

Mean total clock time from PACS send by user to completion of transfer to the DCM4CHEE query/retrieve archive was 5 minutes 32 seconds (+/- SD of 1 min 26 sec). This compares favorably to the report turnaround times for whole-body CT exams, which often exceed 30 minutes. Inference times accounted for most of the total clock time, ranging from 2 minutes 41 seconds to 8 minutes 27 seconds. All other virtual and on-premises host steps combined ranged from a minimum of 34 seconds to a maximum of 48 seconds.

Conclusion

The software worked seamlessly with an existing PACS and could be used for deployment of DL models within the radiology workflow for prospective testing on newly scanned patients. Once configured, the pipeline is executed through one command using a single shell script. The code is made publicly available through an open-source license at "https://github.com/vastc/", and includes a readme file providing pipeline config instructions for host names, series filter, other parameters, and citation instructions for this work.

Self-configuring nnU-net pipeline enables fully automatic infarct segmentation in late enhancement MRI after myocardial infarction

PURPOSE

To fully automatically derive quantitative parameters from late gadolinium enhancement (LGE) cardiac MR (CMR) in patients with myocardial infarction and to investigate if phase sensitive or magnitude reconstructions or a combination of both results in best segmentation accuracy.

METHODS

In this retrospective single center study, a convolutional neural network with a U-Net architecture with a self-configuring framework ("nnU-net") was trained for segmentation of left ventricular myocardium and infarct zone in LGE-CMR. A database of 170 examinations from 78 patients with history of myocardial infarction was assembled. Separate fitting of the model was performed, using phase sensitive inversion recovery, the magnitude reconstruction or both contrasts as input channels. Manual labelling served as ground truth. In a subset of 10 patients, the performance of the trained models was evaluated and quantitatively compared by determination of the Sørensen-Dice similarity coefficient (DSC) and volumes of the infarct zone compared with the manual ground truth using Pearson's r correlation and Bland-Altman analysis.

RESULTS

The model achieved high similarity coefficients for myocardium and scar tissue. No significant difference was observed between using PSIR, magnitude reconstruction or both contrasts as input (PSIR and MAG; mean DSC: 0.83 ± 0.03 for myocardium and 0.72 ± 0.08 for scars). A strong correlation for volumes of infarct zone was observed between manual and model-based approach (r = 0.96), with a significant underestimation of the volumes obtained from the neural network.

CONCLUSION

The self-configuring nnU-net achieves predictions with strong agreement compared to manual segmentation, proving the potential as a promising tool to provide fully automatic quantitative evaluation of LGE-CMR.