2021-02-08 update

In our recent follow-up work, we found that, during the database construction, some tiny outlier annotations were not well removed, which mainly have an effect on the Hausdorff distance metric.

Now, we have corrected these errors and re-evaluated the segmentation performance using the same metrics. We found that there are no changes regarding our findings, but there are some changes in the numerical values of the metrics. We will updated the metrics in the latest version of our paper.

Introduction of CTPelvic1K Dataset

To build a comprehensive pelvic CT dataset that can replicate practical appearance variations, we curate a large dataset of pelvic CT images (CTPelvic1K with 1,184 3D volumes, 320K CT slices) using the following seven sources.

• (Collected) CLINIC and CLINIC-metal. These two sub-datasets are related to pelvic fractures collected from an orthopedic hospital we collaborate with. CLINIC is collected from preoperative images without metal artifact, and CLINIC-metal ismainly collected from postoperative images with metal artifacts.
• (Public) KITS19. This sub-dataset is from the Kits19 challenge ¹³ which is related to kidney and kidney tumor segmentation.
• (Public) CERVIX and ABDOMEN. These two sub-datasets are from the Multi-Atlas Labeling Beyond the Cranial Vault - Workshop and Challenge ³. They are all multi-organ segmentation datasets for different body regions originally.
• (Public) MSD_T10. This sub-dataset comes from the 10th sub-dataset of Medical Segmentation Decathlon ³¹ and features colon tumor segmentation.
• (Public) COLONOG. This sub-dataset comes from the CT COLONOGRAPHY ¹⁶ dataset related to a CT colonography trial. It has prone and supine DICOM images for each patient. We randomly select one of two positions, which have the similar information, of each patient to our large dataset.

KITS19, CERVIX, ABDOMEN, MSD T10, COLONOG, CLINIC, and CLINIC-metal are curated separately from different sites and sources and hence have a diverse range of spacing and FOV. The overview of our large-scale CT Pelvic dataset (CTPelvic1K) and some pelvic CT image examples with various conditions are shown in Table 1 and Fig.1. At the same time, chyme, vascular sclerosis, coprolith, and other situations often encountered in the clinic appear in these sub-datasets. Among them, the data of COLONOG, CLINIC, and CLINIC-metal are stored in a DICOM format, so we can access the information about scanner manufacturer of these sub-datasets.

For more information about CTPelvic1K dataset, please read the following paper. Please also cite this paper if you are using CTPelvic1K dataset for your research!

Pengbo Liu, Hu Han, Yuanqi Du, Heqin Zhu, Yinhao Li, Feng Gu, Honghu Xiao, Jun Li, Chunpeng Zhao, Li Xiao, Xinbao Wu, 
S.Kevin Zhou. Deep Learning to Segment Pelvic Bones: Large-scale CT Datasets and Baseline Models. arXiv: 2012.08721 (2020).

This repository is still work in progress. Annotations will continue to be enriched with other bone structures and other further applications. If you encounter any problems while using CTPelvic1K dataset, please let us know.

Downloading the CTPelvic1K Dataset

In order to facilitate everyone to download the CTPelvic1K and to respect the sub-datasets used in our dataset that have been open-sourced. We upload our work (annotations and new collected clinical data) to a single link and also attach the links of other public datasets used in our whole dataset.

Annotations and new collected clinical data:

Download link: https://zenodo.org/record/4588403#.YEyLq_0zaCo

Because our original annotations are made based on processed dataset (the unrelated areas outside the pelvis are removed), except dataset6 (CLINIC) and dataset7 (CLINIC-metal), we map the annotations back to suit the size of original datasets (1-5). E.g. 'CTPelvic1K_dataset1-5_mask_mappingback.tar.gz' is corresponding to dataset1-5's raw images. For files saved in 'CTPelvic1K_dataset2_mask_mappingback.tar.gz', the naming format is "NumberofPatientNumberofSequence*.nii.gz".

[//]: # (Google Drive link of 'CLINIC', 'CLINIC-metal' and 'CTPelvic1K_dataset1-5_mask_mappingback.tar.gz' : https://drive.google.com/drive/folders/1i5bRyc4Sr1hHQuyPXi16Kc9ZzFal_JeE?usp=sharing)

Public data:

Links to download raw dataset of sub-dataset1-5 used in our CTPelvic1K:

sub-dataset1: ABDOMEN;

sub-dataset2: COLONOG;

sub-dataset3: MSD_T10;

sub-dataset4: KITS19;

sub-dataset5: CERVIX.

Another reason we recommend downloading raw dataset is that the annotations of other bone anatomy are coming. We will merge them all into one file in the future.

Getting Started for Code

All the commands in this section assume that you are in a terminal and your working directory is the CTPelvic1K folder (the one that has all the subfolders like dataset_conversion, evaluation, ...)

And all commands are already writen in CTPelvic1K/nnunet/runs.py.

Table of Contents

• Set paths
• Preparing Datasets & Experiment Planning & Preprocessing
• Experiments
  • Training Models
  • Validation
  • Testing
  • Evaluation
• Results
  • visualization of segmentation results
  • visualization of SDF post-processing results compared with MCR method
• Acknowledgement
• References
• Citation

1 Set paths

Have a look at the file CTPelvic1K/nnunet/paths.py and adapt it to your system by setting the paths where you will store raw data, preprocessed data and trained models.

2 Preparing Datasets & Experiment Planning & Preprocessing

Following commands in runs.py are used for dataset preparing, experiment planning and preprocessing.

home_dir = os.environ['HOME']
train_dir = os.path.join(home_dir,'all_data/nnUNet/rawdata/Task11_CTPelvic1K')
output_dir = os.path.join(home_dir, 'all_data/nnUNet/nnUNet_raw/Task11_CTPelvic1K')
$ command_1 = f'python dataset_conversion/JstPelvisSegmentation_5label.py --train_dir {train_dir} --output_dir {output_dir}'
$ command_2 = 'python experiment_planning/plan_and_preprocess_task.py -t Task11_CTPelvic1K -pl 20 -pf 20'

processed_path = os.path.join(home_dir, 'all_data/nnUNet/nnUNet_processed/Task11_CTPelvic1K')
check_save_path = os.path.join(home_dir, 'all_data/nnUNet/nnUNet_processed/Task11_CTPelvic1K/Task11_check')
$ command_3 = f'python preprocessing/lumbosacral_joint_sampling.py --processed_path {processed_path} --check_save_path {check_save_path}'

os.system(command)

train_dir is where the raw downloaded dataset is stored. command_1 will organize these images and labels to output_dir according to the format of Medical Segmentation Decathlon ¹ datasets.

command_2 will analyze our dataset and determine how to train it bset with nnU-Net models ². Task name (Task11_CTPelvic1K) can be set arbitrarily. -pl/-pf determines how many processes will be used for datatset analysis and preprocessing. Generally you want this number to be as high as you have CPU cores, unless you run into memory problems.

processed_path corresponds to the path storing training/validation data after preprocessing. Due to the serious imbalance between simple areas (anatomy of the bones) and difficult areas (sacroiliac joint and lumbosacral joint), we add oversampling operation for joints region in our experiments. command_3 can extract the coordinates of the target area and save them to the .pkl file (key: "Lumbosacral_Region") of each patient for sampling constraints during training. This imbalance problem mainly appears in 3D fullres scene, because of the high resolution of the CT images, so we only introduce this oversampling operation in 3D fullres (and 3D_cascade), i.e. stage1, experiments.

3 Experiments

The training set, validation set and testing set divisions of our experiments are shown in Table 1 and stored in CTPelvic1K/splits_final.pkl. We set up 22 folds in our experiments, each of which corresponds to an experiment setting (different sub-datasets are included in training phase). Experiments setting of different folds are shown below. For example, we train models on dataset1~6 in fold 0 setting and dataset2-6 (ex dataset1) in fold 7 setting.

3.1 Training Models

parameter settings:
    TASK = 'Task11_CTPelvic1K'
    FOLD = 0
    GPU = 0
$ command_4 = f'python run/run_training.py 2d nnUNetTrainer {TASK} {FOLD} --gpu {GPU}'
$ command_5 = f'python run/run_training.py 3d_fullres nnUNetTrainer {TASK} {FOLD} --gpu {GPU}'
$ command_6 = f'python run/run_training.py 3d_lowres nnUNetTrainer {TASK} {FOLD} --gpu {GPU}'
$ command_7 = f'python run/run_training.py 3d_cascade_fullres nnUNetTrainerCascadeFullRes {TASK} {FOLD} --gpu {GPU}'

nnU-Net ² uses three different U-Net models and can automatically choose which of them to use. We can try them all on our CTPelvic1K dataset.

Trained models are stored in network_training_output_dir (specified in paths.py).

2D U-Net

command_4

3D U-Net (full resolution)

command_5

3D U-Net Cascade

The 3D U-Net cascade only applies to datasets where the patch size possible in the 'fullres' setting is too small relative to the size of the image data. If the cascade was configured you can run it as follows, otherwise this step can be skipped. command_6

After validation these models will automatically also predict the segmentations for the next stage of the cascade and save them in the correct spacing.

Then run: command_7

3.2 Validation

Just add --validation_only to the corresponding training command. --valbest means validating on the best model of validation set during training phase.

$ command_8  = f'python run/run_training.py 2d nnUNetTrainer {TASK} {FOLD} --gpu {GPU} --validation_only --valbest'
$ command_9  = f'python run/run_training.py 3d_fullres nnUNetTrainer {TASK} {FOLD} --gpu {GPU} --validation_only --valbest'
$ command_10 = f'python run/run_training.py 3d_lowres nnUNetTrainer {TASK} {FOLD} --gpu {GPU} --validation_only --valbest'
$ command_11 = f'python run/run_training.py 3d_cascade_fullres nnUNetTrainerCascadeFullRes {TASK} {FOLD} --gpu {GPU} --validation_only --valbest'

3.3 Testing

You can use trained models to predict test data. In order to be able to do so the test data must be provided in the same format as the training data. If you want to use the trained models in the Link above, you should modify the path in the value of key, 'init', in the dict saved as 'model_best.model.pkl'.

test_data_path = os.path.join(home_dir, 'all_data/nnUNet/rawdata/ipcai2021_ALL_Test')

$ command_12 = f'python inference/predict_simple.py ' \
             f'-i {test_data_path} ' \
             f'-o {test_data_path}/{TASK}__{my_output_identifier}__fold{FOLD}_2d_pred ' \
             f'-t {TASK} ' \
             f'-tr nnUNetTrainer ' \
             f'-m 2d ' \
             f'-f {FOLD} ' \
             f'--gpu {GPU}'

$ command_13 = f'python inference/predict_simple.py ' \
              f'-i {test_data_path} ' \
              f'-o {test_data_path}/{TASK}__{my_output_identifier}__fold{FOLD}_3dfullres_pred ' \
              f'-t {TASK} ' \
              f'-tr nnUNetTrainer ' \
              f'-m 3d_fullres ' \
              f'-f {FOLD} ' \
              f'--gpu {GPU}'

$ command_14 = f'python inference/predict_simple.py ' \
              f'-i {test_data_path} ' \
              f'-o {test_data_path}/{TASK}__{my_output_identifier}__fold{FOLD}_3dlowres_pred ' \
              f'-t {TASK} ' \
              f'-tr nnUNetTrainer ' \
              f'-m 3d_lowres ' \
              f'-f {FOLD} ' \
              f'--gpu {GPU} ' \
              f'--overwrite_existing 0'

my_task_lowres = TASK
my_output_identifier_lowres = 'CTPelvic1K' #your low_res experiment\'s "my_output_identifier" in path
$ command_15 = f'python inference/predict_simple.py ' \
              f'-i {test_data_path} ' \
              f'-o {test_data_path}/{TASK}__{my_output_identifier_lowres}__{my_output_identifier}__fold{FOLD}_3dcascadefullres_pred ' \
              f'-t {TASK} ' \
              f'-tr nnUNetTrainerCascadeFullRes ' \
              f'-m 3d_cascade_fullres ' \
              f'-f {FOLD} ' \
              f'-l {test_data_path}/{my_task_lowres}__{my_output_identifier_lowres}__fold{FOLD}_3dlowres_pred ' \
              f'--gpu {GPU} ' \
              f'--overwrite_existing 0'
...

To run inference for 3D U-Net model, use the command_13. If you wish to use the 2D U-Nets, you can set -m 2d instead of 3d_fullres.

To run inference with the cascade, run the following two commands: command_14, command_15. Here we first predict the low resolution segmentations and then use them for the second stage of the cascade.

3.4 Evaluation

$ command_16 = 'python ../evaluation.py'
$ command_17 = 'python ../save_evaluation_results2csv.py'
$ command_18 = 'python ../save_evaluation_results2csv_Manu.py'

command_16 can calculate the metrics (DC/HD) between the prediction results and the ground truth. Then we will get an evaluation*.pkl file that stores all metrics of each patient.

command_17 and command_18 can convert evaluation*.pkl to .csv files for each dataset and manufacturer.

4 Results

4.1 visualization of segmentation results

4.2 visualization of SDF post-processing results compared with MCR method

Large fragments near the anatomical structure are kept with SDF post-processing but are removed by the MCR method.

5 Acknowledgement

Our code is mainly rewritten based on nnU-Net's ^{2, 4} code. Thanks to Febian, et al.'s excellent work, which is a big contribution to the community.

6 References

¹ http://medicaldecathlon.com/
² https://github.com/MIC-DKFZ/nnUNet
³ https://www.synapse.org/#!Synapse:syn3193805/wiki/89480
⁴ Fabian Isensee, Paul F. Jäger, Simon A. A. Kohl, Jens Petersen, Klaus H. Maier-Hein "Automated Design of Deep Learning Methods for Biomedical Image Segmentation" arXiv preprint arXiv:1904.08128 (2020). \ ¹³ Heller, N., Sathianathen, N., et al.: The kits19 challenge data: 300 kidney tumor cases with clinical context, CT semantic segmentations, and surgical outcomes. arXiv:1904.00445 (2019). \ ¹⁶ Johnson, C.D., Chen, M.H., et al.: Accuracy of CT colonography for detection of large adenomas and cancers. New England Journal of Medicine 359(12), 1207{1217 (2008). \ ³¹ Simpson, A.L., Antonelli, M., et al.: A large annotated medical image dataset for the development and evaluation of segmentation algorithms. arXiv:1902.09063 (2019).

7 Citation

If you use our CTPelvic1K dataset, please cite our paper:

Pengbo Liu, Hu Han, Yuanqi Du, Heqin Zhu, Yinhao Li, Feng Gu, Honghu Xiao, Jun Li, Chunpeng Zhao, Li Xiao, Xinbao Wu, 
S.Kevin Zhou. Deep Learning to Segment Pelvic Bones: Large-scale CT Datasets and Baseline Models. arXiv: 2012.08721 (2020).