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About
This is a preprocessed redistribution of Medical Segmentation Decathlon, which is released under the CC BY-SA 4.0 license.
Dataset summary: 1,741 annotated 3D volumes across the 10 Medical Segmentation Decathlon tasks (brain, heart, liver, hippocampus, prostate, lung, pancreas, hepatic vessel, spleen, colon), each with an organ and/or tumour mask.
Contents of this repository:
MSD-BrainTumour/Images-FLAIR/— 484 filesMSD-BrainTumour/Images-T1w/— 484 filesMSD-BrainTumour/Images-T1gd/— 484 filesMSD-BrainTumour/Images-T2w/— 484 filesMSD-BrainTumour/Masks/— 484 filesMSD-Colon/Images/— 126 filesMSD-Colon/Masks/— 126 filesMSD-Heart/Images/— 20 filesMSD-Heart/Masks/— 20 filesMSD-HepaticVessel/Images/— 303 filesMSD-HepaticVessel/Masks/— 303 filesMSD-Hippocampus/Images/— 260 filesMSD-Hippocampus/Masks/— 260 filesMSD-Liver/Images/— 131 filesMSD-Liver/Masks/— 131 filesMSD-Lung/Images/— 63 filesMSD-Lung/Masks/— 63 filesMSD-Pancreas/Images/— 281 filesMSD-Pancreas/Masks/— 281 filesMSD-Prostate/Images-T2w/— 32 filesMSD-Prostate/Images-ADC/— 32 filesMSD-Prostate/Masks/— 32 filesMSD-Spleen/Images/— 41 filesMSD-Spleen/Masks/— 41 files
📝 Landmark annotations, visualization figures and the benchmark plan files live in 🔥MedVision🔥, where you can load the complete images and annotations from dataset configs.
Relation to the source dataset
| In the source | 10 task archives, each shipping a labelled training set (imagesTr/labelsTr) and an unlabelled test set (imagesTs); BrainTumour images are 4-channel and Prostate images 2-channel 4D NIfTI |
| Excluded here | the unlabelled imagesTs volumes of all 10 tasks (no public masks), and the per-task dataset.json |
| In this repo | 484 MSD-BrainTumour/Images-FLAIR + 484 MSD-BrainTumour/Images-T1w + 484 MSD-BrainTumour/Images-T1gd + 484 MSD-BrainTumour/Images-T2w + 484 MSD-BrainTumour/Masks + 126 MSD-Colon/Images + 126 MSD-Colon/Masks + 20 MSD-Heart/Images + 20 MSD-Heart/Masks + 303 MSD-HepaticVessel/Images + 303 MSD-HepaticVessel/Masks + 260 MSD-Hippocampus/Images + 260 MSD-Hippocampus/Masks + 131 MSD-Liver/Images + 131 MSD-Liver/Masks + 63 MSD-Lung/Images + 63 MSD-Lung/Masks + 281 MSD-Pancreas/Images + 281 MSD-Pancreas/Masks + 32 MSD-Prostate/Images-T2w + 32 MSD-Prostate/Images-ADC + 32 MSD-Prostate/Masks + 41 MSD-Spleen/Images + 41 MSD-Spleen/Masks |
Every labelled case of all 10 tasks is included - 1,741 cases. No format conversion was required: the source already ships nii.gz, and image and mask voxel data are carried over unmodified. What is derived here is the RAS+ reorientation, the MSD-<Task>/{Images,Masks} layout, and the splitting of the 4D multi-channel volumes into one 3D volume per channel.
Because of that split, two tasks have no plain Images/ folder: MSD-BrainTumour ships Images-FLAIR, Images-T1w, Images-T1gd, Images-T2w and MSD-Prostate ships Images-T2w, Images-ADC. Each of those tasks still has a single Masks/ folder, which pairs case-for-case with every one of its modality folders.
Why -Lite? The suffix marks this as a derived redistribution rather than a copy of the source. These are preprocessed volumes — every case has been format-converted where needed, geometry-normalised and reoriented to RAS+ — and for some sources cases or modalities are excluded as well (see the table above). Use it to reproduce MedVision, not as a substitute for the original release. See Preprocessing below for exactly what was changed.
Preprocessing
Built from the 10 official task archives (
Task01_BrainTumour.tar...Task10_Colon.tar) athttps://msd-for-monai.s3-us-west-2.amazonaws.com.Task0N_<X>/is renamed toMSD-<X>/,imagesTr/toImages/andlabelsTr/toMasks/; the unlabelledimagesTs/and the per-taskdataset.jsonare dropped.4D multi-channel images are split into one 3D volume per channel: BrainTumour into
Images-FLAIR/Images-T1w/Images-T1gd/Images-T2w(channel order as published), Prostate intoImages-T2w/Images-ADC. The mask is not duplicated per channel.macOS resource forks and metadata from the source archives (
._*,.DS_Store) are removed.No format conversion and no resampling - labels are the source's. Only the orientation is standardized to RAS+.
📝 ShareAlike. MSD is CC BY-SA 4.0, so this mirror is redistributed under the same licence, the modifications made are stated above, and no additional restrictions are imposed - the repository is public and ungated, and any redistribution of it or of a derivative must stay that way. Note also that several MSD tasks are re-cropped by other public collections (e.g. ULS23 re-uses MSD lesions), so combining MSD with such a dataset can place the same lesion on both sides of a train/test split.
Segmentation Labels
labels_map_MSD_BrainTumour = {
"1": "edema of brain",
"2": "non-enhancing brain tumor",
"3": "enhancing brain tumor"
}
labels_map_MSD_Colon = {
"1": "colon cancer primaries"
}
labels_map_MSD_HepaticVessel = {
"1": "liver vessel",
"2": "liver tumor"
}
labels_map_MSD_Liver = {
"1": "liver",
"2": "liver cancer"
}
labels_map_MSD_Lung = {
"1": "lung cancer"
}
labels_map_MSD_Pancreas = {
"1": "pancreas",
"2": "pancreas cancer"
}
labels_map_MSD_Heart = {
"1": "left atrium of heart"
}
labels_map_MSD_Hippocampus = {
"1": "anterior hippocampus",
"2": "posterior hippocampus"
}
labels_map_MSD_Prostate = {
"1": "peripheral zone of prostate",
"2": "transition zone of prostate"
}
labels_map_MSD_Spleen = {
"1": "spleen"
}
Landmarks
landmarks_map = {
"P1": "most right/anterior/superior endpoint of the major axis",
"P2": "most left/superior/inferior endpoint of the major axis",
"P3": "most right/anterior/superior endpoint of the minor axis",
"P4": "most left/superior/inferior endpoint of the minor axis"
}
News
[2 Aug, 2026] Initial release. This dataset is integrated into 🔥MedVision🔥, where you can use these config names to load data in python:
MSD_BoxSize_Task01_Axial_TestMSD_BoxSize_Task01_Axial_TrainMSD_BoxSize_Task01_Coronal_TestMSD_BoxSize_Task01_Coronal_TrainMSD_BoxSize_Task01_Sagittal_TestMSD_BoxSize_Task01_Sagittal_TrainMSD_BoxSize_Task02_Axial_TestMSD_BoxSize_Task02_Axial_TrainMSD_BoxSize_Task02_Coronal_TestMSD_BoxSize_Task02_Coronal_TrainMSD_BoxSize_Task02_Sagittal_TestMSD_BoxSize_Task02_Sagittal_TrainMSD_BoxSize_Task03_Axial_TestMSD_BoxSize_Task03_Axial_TrainMSD_BoxSize_Task03_Coronal_TestMSD_BoxSize_Task03_Coronal_TrainMSD_BoxSize_Task03_Sagittal_TestMSD_BoxSize_Task03_Sagittal_TrainMSD_BoxSize_Task04_Axial_TestMSD_BoxSize_Task04_Axial_TrainMSD_BoxSize_Task04_Coronal_TestMSD_BoxSize_Task04_Coronal_TrainMSD_BoxSize_Task04_Sagittal_TestMSD_BoxSize_Task04_Sagittal_TrainMSD_BoxSize_Task05_Axial_TestMSD_BoxSize_Task05_Axial_TrainMSD_BoxSize_Task05_Coronal_TestMSD_BoxSize_Task05_Coronal_TrainMSD_BoxSize_Task05_Sagittal_TestMSD_BoxSize_Task05_Sagittal_TrainMSD_BoxSize_Task06_Axial_TestMSD_BoxSize_Task06_Axial_TrainMSD_BoxSize_Task06_Coronal_TestMSD_BoxSize_Task06_Coronal_TrainMSD_BoxSize_Task06_Sagittal_TestMSD_BoxSize_Task06_Sagittal_TrainMSD_BoxSize_Task07_Axial_TestMSD_BoxSize_Task07_Axial_TrainMSD_BoxSize_Task07_Coronal_TestMSD_BoxSize_Task07_Coronal_TrainMSD_BoxSize_Task07_Sagittal_TestMSD_BoxSize_Task07_Sagittal_TrainMSD_BoxSize_Task08_Axial_TestMSD_BoxSize_Task08_Axial_TrainMSD_BoxSize_Task08_Coronal_TestMSD_BoxSize_Task08_Coronal_TrainMSD_BoxSize_Task08_Sagittal_TestMSD_BoxSize_Task08_Sagittal_TrainMSD_BoxSize_Task09_Axial_TestMSD_BoxSize_Task09_Axial_TrainMSD_BoxSize_Task09_Coronal_TestMSD_BoxSize_Task09_Coronal_TrainMSD_BoxSize_Task09_Sagittal_TestMSD_BoxSize_Task09_Sagittal_TrainMSD_BoxSize_Task10_Axial_TestMSD_BoxSize_Task10_Axial_TrainMSD_BoxSize_Task10_Coronal_TestMSD_BoxSize_Task10_Coronal_TrainMSD_BoxSize_Task10_Sagittal_TestMSD_BoxSize_Task10_Sagittal_TrainMSD_BoxSize_Task11_Axial_TestMSD_BoxSize_Task11_Axial_TrainMSD_BoxSize_Task11_Coronal_TestMSD_BoxSize_Task11_Coronal_TrainMSD_BoxSize_Task11_Sagittal_TestMSD_BoxSize_Task11_Sagittal_TrainMSD_BoxSize_Task12_Axial_TestMSD_BoxSize_Task12_Axial_TrainMSD_BoxSize_Task12_Coronal_TestMSD_BoxSize_Task12_Coronal_TrainMSD_BoxSize_Task12_Sagittal_TestMSD_BoxSize_Task12_Sagittal_TrainMSD_BoxSize_Task13_Axial_TestMSD_BoxSize_Task13_Axial_TrainMSD_BoxSize_Task13_Coronal_TestMSD_BoxSize_Task13_Coronal_TrainMSD_BoxSize_Task13_Sagittal_TestMSD_BoxSize_Task13_Sagittal_TrainMSD_BoxSize_Task14_Axial_TestMSD_BoxSize_Task14_Axial_TrainMSD_BoxSize_Task14_Coronal_TestMSD_BoxSize_Task14_Coronal_TrainMSD_BoxSize_Task14_Sagittal_TestMSD_BoxSize_Task14_Sagittal_TrainMSD_MaskSize_Task01_Axial_TestMSD_MaskSize_Task01_Axial_TrainMSD_MaskSize_Task01_Coronal_TestMSD_MaskSize_Task01_Coronal_TrainMSD_MaskSize_Task01_Sagittal_TestMSD_MaskSize_Task01_Sagittal_TrainMSD_MaskSize_Task02_Axial_TestMSD_MaskSize_Task02_Axial_TrainMSD_MaskSize_Task02_Coronal_TestMSD_MaskSize_Task02_Coronal_TrainMSD_MaskSize_Task02_Sagittal_TestMSD_MaskSize_Task02_Sagittal_TrainMSD_MaskSize_Task03_Axial_TestMSD_MaskSize_Task03_Axial_TrainMSD_MaskSize_Task03_Coronal_TestMSD_MaskSize_Task03_Coronal_TrainMSD_MaskSize_Task03_Sagittal_TestMSD_MaskSize_Task03_Sagittal_TrainMSD_MaskSize_Task04_Axial_TestMSD_MaskSize_Task04_Axial_TrainMSD_MaskSize_Task04_Coronal_TestMSD_MaskSize_Task04_Coronal_TrainMSD_MaskSize_Task04_Sagittal_TestMSD_MaskSize_Task04_Sagittal_TrainMSD_MaskSize_Task05_Axial_TestMSD_MaskSize_Task05_Axial_TrainMSD_MaskSize_Task05_Coronal_TestMSD_MaskSize_Task05_Coronal_TrainMSD_MaskSize_Task05_Sagittal_TestMSD_MaskSize_Task05_Sagittal_TrainMSD_MaskSize_Task06_Axial_TestMSD_MaskSize_Task06_Axial_TrainMSD_MaskSize_Task06_Coronal_TestMSD_MaskSize_Task06_Coronal_TrainMSD_MaskSize_Task06_Sagittal_TestMSD_MaskSize_Task06_Sagittal_TrainMSD_MaskSize_Task07_Axial_TestMSD_MaskSize_Task07_Axial_TrainMSD_MaskSize_Task07_Coronal_TestMSD_MaskSize_Task07_Coronal_TrainMSD_MaskSize_Task07_Sagittal_TestMSD_MaskSize_Task07_Sagittal_TrainMSD_MaskSize_Task08_Axial_TestMSD_MaskSize_Task08_Axial_TrainMSD_MaskSize_Task08_Coronal_TestMSD_MaskSize_Task08_Coronal_TrainMSD_MaskSize_Task08_Sagittal_TestMSD_MaskSize_Task08_Sagittal_TrainMSD_MaskSize_Task09_Axial_TestMSD_MaskSize_Task09_Axial_TrainMSD_MaskSize_Task09_Coronal_TestMSD_MaskSize_Task09_Coronal_TrainMSD_MaskSize_Task09_Sagittal_TestMSD_MaskSize_Task09_Sagittal_TrainMSD_MaskSize_Task10_Axial_TestMSD_MaskSize_Task10_Axial_TrainMSD_MaskSize_Task10_Coronal_TestMSD_MaskSize_Task10_Coronal_TrainMSD_MaskSize_Task10_Sagittal_TestMSD_MaskSize_Task10_Sagittal_TrainMSD_MaskSize_Task11_Axial_TestMSD_MaskSize_Task11_Axial_TrainMSD_MaskSize_Task11_Coronal_TestMSD_MaskSize_Task11_Coronal_TrainMSD_MaskSize_Task11_Sagittal_TestMSD_MaskSize_Task11_Sagittal_TrainMSD_MaskSize_Task12_Axial_TestMSD_MaskSize_Task12_Axial_TrainMSD_MaskSize_Task12_Coronal_TestMSD_MaskSize_Task12_Coronal_TrainMSD_MaskSize_Task12_Sagittal_TestMSD_MaskSize_Task12_Sagittal_TrainMSD_MaskSize_Task13_Axial_TestMSD_MaskSize_Task13_Axial_TrainMSD_MaskSize_Task13_Coronal_TestMSD_MaskSize_Task13_Coronal_TrainMSD_MaskSize_Task13_Sagittal_TestMSD_MaskSize_Task13_Sagittal_TrainMSD_MaskSize_Task14_Axial_TestMSD_MaskSize_Task14_Axial_TrainMSD_MaskSize_Task14_Coronal_TestMSD_MaskSize_Task14_Coronal_TrainMSD_MaskSize_Task14_Sagittal_TestMSD_MaskSize_Task14_Sagittal_TrainMSD_TumorLesionSize_Task01_Axial_TestMSD_TumorLesionSize_Task01_Axial_TrainMSD_TumorLesionSize_Task01_Coronal_TestMSD_TumorLesionSize_Task01_Coronal_TrainMSD_TumorLesionSize_Task01_Sagittal_TestMSD_TumorLesionSize_Task01_Sagittal_TrainMSD_TumorLesionSize_Task02_Axial_TestMSD_TumorLesionSize_Task02_Axial_TrainMSD_TumorLesionSize_Task02_Coronal_TestMSD_TumorLesionSize_Task02_Coronal_TrainMSD_TumorLesionSize_Task02_Sagittal_TestMSD_TumorLesionSize_Task02_Sagittal_TrainMSD_TumorLesionSize_Task03_Axial_TestMSD_TumorLesionSize_Task03_Axial_TrainMSD_TumorLesionSize_Task03_Coronal_TestMSD_TumorLesionSize_Task03_Coronal_TrainMSD_TumorLesionSize_Task03_Sagittal_TestMSD_TumorLesionSize_Task03_Sagittal_TrainMSD_TumorLesionSize_Task04_Axial_TestMSD_TumorLesionSize_Task04_Axial_TrainMSD_TumorLesionSize_Task04_Coronal_TestMSD_TumorLesionSize_Task04_Coronal_TrainMSD_TumorLesionSize_Task04_Sagittal_TestMSD_TumorLesionSize_Task04_Sagittal_TrainMSD_TumorLesionSize_Task05_Axial_TestMSD_TumorLesionSize_Task05_Axial_TrainMSD_TumorLesionSize_Task05_Coronal_TestMSD_TumorLesionSize_Task05_Coronal_TrainMSD_TumorLesionSize_Task05_Sagittal_TestMSD_TumorLesionSize_Task05_Sagittal_TrainMSD_TumorLesionSize_Task06_Axial_TestMSD_TumorLesionSize_Task06_Axial_TrainMSD_TumorLesionSize_Task06_Coronal_TestMSD_TumorLesionSize_Task06_Coronal_TrainMSD_TumorLesionSize_Task06_Sagittal_TestMSD_TumorLesionSize_Task06_Sagittal_TrainMSD_TumorLesionSize_Task07_Axial_TestMSD_TumorLesionSize_Task07_Axial_TrainMSD_TumorLesionSize_Task07_Coronal_TestMSD_TumorLesionSize_Task07_Coronal_TrainMSD_TumorLesionSize_Task07_Sagittal_TestMSD_TumorLesionSize_Task07_Sagittal_TrainMSD_TumorLesionSize_Task08_Axial_TestMSD_TumorLesionSize_Task08_Axial_TrainMSD_TumorLesionSize_Task08_Coronal_TestMSD_TumorLesionSize_Task08_Coronal_TrainMSD_TumorLesionSize_Task08_Sagittal_TestMSD_TumorLesionSize_Task08_Sagittal_Train
Data Usage Agreement
By using the dataset, you agree to the terms as follow.
- You must comply with the original
CC BY-SA 4.0license terms of the source dataset. - You are recommended to refer to the source of this dataset in any publication:
https://huggingface.co/datasets/YongchengYAO/MSD-Lite - You must cite the original publication(s):
Official Release
For more information, please go to the official site: http://medicaldecathlon.com/dataaws/
Download from Huggingface
# python
from huggingface_hub import snapshot_download
snapshot_download(repo_id="YongchengYAO/MSD-Lite", repo_type='dataset', local_dir="/your/local/folder")
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