Numerous auto-segmentation methods exist for Organs at Risk in radiotherapy. The overall objective of this auto-segmentation grand challenge is to provide a platform for comparison of various auto-segmentation algorithms when they are used to delineate organs at risk (OARs) from CT images for thoracic patients in radiation treatment planning. The results will provide an indication of the performances achieved by various auto-segmentation algorithms and can be used to guide the selection of these algorithms for clinic use if desirable. The challenge is made up of multiple phases:
Phase 1 will conducted via this website in advance of the AAPM meeting. 12 test images will be provided and results will be submitted online. The 3 top place contestants in this phase will be invited to present at the challenge symposium at AAPM.
Phase 2 will be conducted live at the AAPM. A further 12 test images will be provided for evaluation, and participants will have 2 hours to generate results. Participants need not have participated in Phase 1 to be part of Phase 2.
Symposium Following Phase 2 a symposium will be held at which the results of both previous phases will be presented.
Phase 3 will be an on-going benchmarking conducted via this website. Both test sets from phase 1 and 2 will be included within the on-going assessment.
The top 3 participants in the Pre-AAPM challenge will be invited to present at the Challenge Symposium at the AAPM 2017 Annual Meeting.
The top 3 participants in the AAPM live challenge will receive conference registration reimbursement and a certificate of merit from AAPM.
The live challenge winners were announced at the challenge symposium at the 2017 AAPM annual meeting. This AAPM Newsletter article also reported this challenge and the winners.
Standard name: Esophagus
RTOG Atlas description: The esophagus should be contoured from the beginning at the level just below the cricoid to its entrance to the stomach at GE junction. The esophagus will be contoured using mediastinal window/level on CT to correspond to the mucosal, submucosa, and all muscular layers out to the fatty adventitia.
Additional notes: The superior-most slice of the esophagus is the slice below the first slice where the lamina of the cricoid cartilage is visible (+/- 1 slice). The inferior-most slice of the esophagus is the first slice (+/- 1 slice) where the esophagus and stomach are joined, and at least 10 square cm of stomach cross section is visible.
Standard name: Heart
RTOG Atlas description: The heart will be contoured along with the pericardial sac. The superior aspect (or base) will begin at the level of the inferior aspect of the pulmonary artery passing the midline and extend inferiorly to the apex of the heart.
Additional notes: Inferior vena cava is excluded or partly excluded starting at slice where at least half of the circumference is separated from the right atrium.
Standard names: Lung_L, Lung_R
RTOG Atlas description: Both lungs should be contoured using pulmonary windows. The right and left lungs can be contoured separately, but they should be considered as one structure for lung dosimetry. All inflated and collapsed, fibrotic and emphysematic lungs should be contoured, small vessels extending beyond the hilar regions should be included; however, pre GTV, hilars and trachea/main bronchus should not be included in this structure.
Additional notes: Tumor is excluded in most data, but size and extent of excluded region are not guaranteed. Hilar airways and vessels greater than 5 mm (+/- 2 mm) diameter are excluded. Main bronchi are always excluded, secondary bronchi may be included or excluded. Small vessels near hilum are not guaranteed to be excluded. Collapsed lung may be excluded in some scans. Regions of tumor or collapsed lung that are excluded from training and test data will be masked out during evaluation, such that scores are affected by segmentation choices in those regions.
Standard name: SpinalCord
RTOG Atlas description: The spinal cord will be contoured based on the bony limits of the spinal canal. The spinal cord should be contoured starting at the level just below cricoid (base of skull for apex tumors) and continuing on every CT slice to the bottom of L2. Neuroformanines should not be included.
Additional notes: Spinal cord may be contoured beyond cricoid superiorly, and beyond L2 inferiorly. Contouring to base of skull is not guaranteed for apical tumors.
Auto-segmented contours will be compared against the manual contours for all test datasets using the following evaluation metrics as implemented in Plastimatch. RTSS will be voxelised to CT resolution for all calculations. Evaluation will be performed in 3D. To prevent uncertainty with the extent to which the Spinal cord and Esophagus should be contoured, submitted contours will be cropped to the extent of the test data. Therefore, you will not be penalised for contouring too great an extent of the structure in the inferior-superior direction, but will for under-segmentation.
This is a measure of relative overlap, where 1 represents perfect agreement and 0 represents no overlap.
where X and Y are the ground truth and test regions.
Mean surface distance
The directed average Hausdorff measure is the average distance of a point in X to its closest point in Y. That is:
The (undirected) average Hausdorff measure is the average of the two directed average Hausdorff measures:
Hausdorff distance (95% Hausdorff distance)
The directed percent Hausdorff measure, for a percentile r, is the r th percentile distance over all distances from points in X to their closest point in Y. For example, the directed 95% Hausdorff distance is the point in X with distance to its closest point in Y is greater or equal to exactly 95% of the other points in X. In mathematical terms, denoting the r th percentile as Kr, this is given as:
The (undirected) percent Hausdorff measure is defined again with the mean:
Normalisation of the score
Different organs and measures will have different ranges of scores, therefore it is not possible to simply average them to get an overall score. Therefore to be able to normalise the scores with respect to expected values 3 cases have been contoured by multiple observers. The mean score of these observers will be used as a reference score against which submitted contours will be compared. For any organ/measure a perfect value(Dice = 1, AD/HD =0) will be scored 100. A value equivalent to the average inter-observer reference will be given a score of 50. A linear scale will be used to interpolate between these values, and extrapolate beyond them, such that a score of 0 will be given to any result below the reference by more than the perfect score is above the reference.
Score = max ( 50 + ( (T-R)/(P-R) * 50 ), 0 )
Where T is the test contour measure, P is the perfect measure, and R is the reference measure for that organ/measure.
For example, given a reference Dice of 0.85; a test contour with a Dice of 0.9 against the "ground truth" will score 66.6, where as a test contour with a Dice of 0.72 against the "ground truth" would score 7.
The normalized scores for all organs, measure and test cases will be averaged (mean) to give a final score. The winner will be the team with the highest final score.
Submitted contours should include all of the the structures found in the training data, named in the same way as the training data. i.e. each case should contain:
The results should be submitted as a single DICOM RTSTRUCT file per test case. Each file should be named according to the patient ID for the case - i.e. LCTSC-Test-S1-101.dcm
Structure files for all 12 test cases should encapsulated into a single zip file. There must be no folder structure within the zip file. No specific naming is required for the zip file. This zip file can then be uploaded via the participate page.
If you have file naming errors, files missing, structure naming errors the website should report these to you, but may result in that submission being scored zero.
Below is the instruction of using 3D Slicer to perform the conversion:
1) Load all images. At time of load, click "Labelmap" checkbox for each structure
2) Go to Segmentation module
3) For "Active segmentation", choose "Create new segmentation"
4) For each structure, repeat:
4a) In "Export/Import segments", choose structure, and import as labelmap
5) Click on one of the segments, and then click "Edit selected"
6) Set the "Master volume" to your CT
7) Go to Data module.
8) On background, right click choose "Create new subject"
9) On subject, right click choose "Create child study"
10) Drag the CT and segmentation node onto the child study
11) Right click on study, choose "Export to DICOM"
12) Enjoy your newly created DICOM-RT file
Please submit your off-site test results to enter the live competition. The live competition of this grand challenge will be held in conjunction with the 2017 AAPM annual meeting, which will be held at the Colorado convention center at 700 14th street, Denver, Colorado, USA. Meeting information is available here. Please register for the meeting for the live competition.
The live competition will be held 1:45PM-3:45PM on Wednesday, August 2nd, 2017 in room 612. Please arrive no later than 1:30PM so you have enough time to set up your computer. You will need to bring your own laptop for the live challenge. The live challenge data will be distributed using a USB drive. You will need to complete the segmentation and submit the results within 2 hours. There will be no dedicated internet drop for each laptop. You may use the AAPM Wi-Fi for internet access (about 2Mbps Up/Down). Please be advised that the Wi-Fi connection may not be reliable.
Please use the same submission guidelines for the off-site test. The results should be submitted as a single DICOM RTSTRUCT file per test case. Each file should be named according to the patient ID for the case. We will collect your entry via USB to ensure its successful submission.
The challenge symposium will be held 10:00AM-12:00AM on Thursday, August 3rd, 2017 in room Four Seasons 2. The live competition winners will be announced and invited to a round table discussion following the oral presentations by the top participants in the off-site challenge . The top 3 winners in the live competition will receive conference registration reimbursement and a certificate of merit from AAPM. The customized certificate of merit will be mailed to the winners after the AAPM meeting.
Participants who cannot attend the AAPM meeting are allowed to remotely participate in the live competition, but will not be eligible for awards. The live test data will be made available on the website at the beginning of the live competition (around 1:45PM Mountain Time, August 2nd, 2017). Remote participants should submit their results directly to the online evaluation system. Only one submission is allowed within 24 hours. The scores from remote participants will be presented at the challenge symposium if it is available before the symposium (10:00AM Mountain Time, August 3rd, 2017).
Please login to your account to learn the options to obtain the live competition data.
Start: May 18, 2017, midnight
Description: Participants download the training data with ground truth to train and optimize their algorithms for the segmentation task.
Start: June 19, 2017, midnight
Description: Participants perform segmentation on the off-site test data and submit their results to compete for the three seats to present their work at Challenge Symposium at the AAPM 2017 Annual Meeting.
Start: Aug. 2, 2017, midnight
Description: Participants perform segmentation on the live test data at the AAPM 2017 Annual Meeting to win the Challenge and awards from AAPM.
Start: Aug. 4, 2017, midnight
Description: Participants interested in evaluating their algorithms can submit their results for both off-site and live test data in one place.
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