fidoptPancreas-CT, 8 organs
Contrast-enhanced abdominal CT of two patients of the NIH Clinical Center in the portal-venous phase (Pancreas-CT), with eight organs labelled by Gibson et al., paired by us.
Read before comparing (8)
- Cohort. Patients scanned at the NIH Clinical Center about 70 seconds after a contrast injection: 17 healthy kidney donors and patients with neither a major abdominal disease nor a pancreatic cancer lesion. The files say neither which is which nor the patients' sex or age.
- Truth. Gibson et al. drew the seven organs the collection lacks, an image research fellow supervised by a radiologist, and edited the collection's pancreas so that all eight follow one protocol.
- Gaps. The labels may be incomplete outside the box each scan was cropped to in its paper (cropping.csv); they are kept as delivered. The oesophagus is labelled only from about the top of the liver down, on every scan alike. Patient 0032 has no gallbladder label, so 0044_0032 is scored on seven organs.
- Alignment. The scans carry no position of their own, each origin at zero, at a corner of its top slice, and keep their native voxels. The moving header carries one elastix translation on mutual information inside each body, the best of several starts, no annotation used. A rigid fit turns the bodies 2.9 to 9.6 degrees on the test pairs, so only the translation is kept.
- Baseline. With no registration the 10 test pairs start at a Dice of 0.28 (0.13 to 0.49), against 0.19 as delivered and 0.35 after a fit on the organ centres, and an HD95 of 40 mm (19 to 63). On 0011_0030 the larger moving body leaves the spines a centimetre or two apart. The size difference between two patients is left to the methods.
- Overlap. Patient 0025 is left out: TCIA removed it as the same scan as patient 0002, cropped otherwise. No other dataset of the corpus holds these scans: L2R_AbdomenCTCT comes from BTCV, scanned at Vanderbilt University Medical Center, and PancreaticCTCBCT holds patients treated for a pancreatic cancer.
- Images. The slices are 1 mm apart (0.5 mm on patient 0044), where the collection gives a thickness of 1.5 to 2.5 mm. Five of the 26 scans built read -2048 outside the field of view, the others -1024, as delivered.
- Outside numbers. None: the pairing is ours.
| Accuracy | Smoothness | Cost | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| # | Method | Dice | Change | HD95 mm | SDlogJ | Folds % | Time s | RAM GB | GPU GB | Images |
| 1 | DemonsCPUapp | 0.368 ±0.111 | +0.085 | 37.62 ±9.82 | 0.084 | 0.08 | 53 | 8.6 | ||
| No registration | 0.283 ±0.080 | 40.42 ±9.65 | 0.000 | 0.00 | ||||||
The order averages each method's ranks on Dice, HD95 mm, SDlogJ, so the first one is not always the best in every column. ± is the 95% interval of the mean over the 10 pairs. Two neighbours are tied when a paired Wilcoxon test on the shared pairs does not find the upper one better on Dice (5%): the places a method could hold are then shown under its own. The best value of each column is in colour. Click a row to see its images, a column title to sort by it. Time and memory measured on Laptop.
1 result not ranked: an older run, pairs still missing, or a failure on every pair
| Accuracy | Smoothness | Cost | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| # | Method | Dice | Change | HD95 mm | SDlogJ | Folds % | Time s | RAM GB | GPU GB | Machine | Images |
| ConvexAdam (MIND)GPUapp9/10 pairs | 0.382 ±0.112 | +0.099 | 38.10 ±10.90 | 0.121 | 0.79 | 49 | 5.7 | 15.1 | Laptop | ||
Dice: how much the organ contours overlap, 1 is perfect. HD95: distance between the contours' surfaces. SDlogJ: how irregular the deformation is, 0 is perfectly smooth. Folds: share of the image where the deformation folds over itself.
Pair by pair
Click a score to look at that result: the fixed image, and over it the moving image after registration, with the annotations. Underlined scores have their image; for the others you see the pair without the result. A green cell gained against no registration on that pair, a red one lost.
About the data
- Test pairs
- 10 test pairs drawn with seed 2026 among the 11 outside development, and 10 development pairs. prepare.py puts the 42 patients with labels in the seed's order and pairs them two by two.
- Truth
- contours by experts 8 organs, Gibson et al.'s reference segmentations: spleen, left kidney, gallbladder, oesophagus, liver, stomach, pancreas, duodenum
- Source
- www.cancerimagingarchive.net/collection/pancreas-ct
doi.org/10.7937/K9/TCIA.2016.tNB1kqBU
zenodo.org/records/1169361
doi.org/10.1109/TMI.2018.2806309 - Licence
- CC BY 3.0 (images), CC BY 4.0 (labels)
10 pairs for tuning, never tested
0004_0047, 0005_0013, 0008_0022, 0048_0012, 0029_0043, 0017_0003, 0042_0040, 0021_0031, 0034_0045, 0018_0046