Awesome

Update 8/29/2024

Our paper has been accepted by MICCAI 2024 Open Data for oral presentation. Meanwhile, we uploaded our dataset to the AFRICAI repository of XNAT, where we recommend downloading all CT images and annotations.

Update 1/21/2022

We uploaded the data_split file to data_split.txt, which splits the dataset into trainset, test_public, and test_private, as our paper described. Meanwhile, we uploaded this file to Baiduyun.

Update 7/5/2021

Note that for the VerSe dataset, partially visible vertebrae at the top or bottom of the scan (or both) were not annotated. In contrast, CTSpine1K annotated them, which caused the situation in our previous version paper; the reported dice value on the VerSe dataset is much lower than on the CTSpine1K dataset (0.619 VS 0.840). Therefore, we annotated all visible vertebrae (see figure below) and recalculated the metrics(0.766 VS 0.840).

We have updated our paper on arxiv and uploaded the completed annotations for the VerSe dataset to Google Drive Google Drive and Baiduyun (password： send email to dengy066@gmail.com).

Note: only annotations were uploaded to Google Drive due to the limited free storage space, and you need to download the original CT images from the responding websites.

Besides, we updated a more specific biconcave fracture case in Figure 1(F).

Update 6/11/2021

We uploaded Path.csv to clarify the CT positions we used for the COLONOG dataset and HNSCC-3DCT-RT dataset and deleted the dicom2nii.py file. We also upload the original CT images to Baiduyun (password：send email to dengy066@gmail.com)

Introduction for the CTSpine1K dataset

To advance the research in spinal image analysis, we hereby present a large-scale and comprehensive dataset: CTSpine1K. To build a comprehensive spine dataset replicating practical appearance variations, we curate CTSpine1K from the following four open sources, totaling 1,005 CT volumes (over 500,000 labeled slices and over 11,000 vertebrae) of diverse appearance variations.

*COLONOG. This sub-dataset comes from the CT COLONOGRAPHY dataset related to a CT colonography trial12. We randomly select one of the two positions (we open the code for selecting them, dicom2nii.py), with similar information for each patient for our dataset . There are 825 CT scans, and they are in Digital Imaging and Communication in Medicine (DICOM) format.

*HNSCC-3DCT-RT. This sub-dataset contains three-dimensional (3D) high-resolution fan-beam CT scans collected during pre-treatment, mid-treatment, and post-treatment using a Siemens 16-slice CT scanner with the standard clinical protocol for head-and-neck squamous cell carcinoma (HNSCC) patients13. These images are in DICOM format.

*MSD T10. This sub-dataset comes from the 10th Medical Segmentation Decathlon14. To attain more slices containing the spine, we select the task03_liver dataset consisting of 201 cases. These images are in Neuroimaging Informatics Technology Initiative (NIfTI) format (https://nifti.nimh.nih.gov/nifti-1).

*COVID-19. This sub-dataset consists of non-enhanced chest CTs from 632 patients with COVID-19 infections. The images were acquired at the point of care in an outbreak setting from patients with Reverse Transcription Polymerase Chain Reaction(RT-PCR) confirmation for the presence of SARS-CoV-215. We pick 40 scans with the images stored in NIfTI format.

We reformat all DICOM images to NIfTI to simplify data processing and de-identify images, meeting the institutional review board (IRB) policies of contributing sites. More details for those sub-datasets can be found in12–15. All existing sub-datasets are under Creative Commons license CC-BY-NC-SA and we will keep the license unchanged. It should be noted that for sub-dataset task03_liver and sub-dataset COVID-19, we only choose a part of cases from them, and in all these data sources, we exclude those cases of very low quality. The overview of our dataset and the thorough comparison with the VerSe Challenge dataset (We only chose those samples that are not cropped) can be seen in Table 1.

For more information about the CTSpine1K dataset, please read the following paper. Please also cite this paper if you are using the CTSpine1K dataset for your research.

Yang Deng, Ce Wang, Yuan Hui, et al. CtSpine1k: A large-scale dataset for spinal vertebrae segmentation in computed tomography. arXiv preprint arXiv:2105.14711 (2021). 

Downloading the CTSpine1K Dataset

The original images can be downloaded from the corresponding URL above.

The segmentation masks and the pre-trained model are on Google Drive or Baiduyun (password： send email to dengy066@gmail.com)

Annotation pipeline with nnUnet

Follow https://github.com/MIC-DKFZ/nnUNet/commit/058b695d61d34dda7f79cd36ab950a5d3e031653 to set and use nnUnet. The specific usage here can be seen in the ReadMe.md file. Our annotation pipeline is presented in Figure 2 below.

Benchmarking results

The benchmarking results are shown in Table 2.

Acknowledgement

Thank Febian's nnUnet and we appreciate the open-source sub-datasets we used.

Thank Jianji Wang and Guoxin Fan(MD) for their help in Fig.1(F)

Please feel free to email dengy066@gmail.com if you have any question.