| --- |
| license: cc-by-4.0 |
| task_categories: |
| - image-feature-extraction |
| language: |
| - en |
| tags: |
| - medical |
| - image |
| - mri |
| - brain |
| - landmarks |
| - biometry |
| pretty_name: 'afids-lite' |
| size_categories: |
| - n<1K |
| --- |
| |
|
|
| ## About |
| This is a preprocessed redistribution of [AFIDs](https://github.com/afids/afids-data) (OpenNeuro `ds004470` + `ds004471`), which is released under the `CC BY 4.0` license. |
|
|
| **Dataset summary:** 72 T1-weighted brain MR scans with 32 anatomical fiducial (AFID) landmarks each. |
|
|
| **Contents of this repository:** |
|
|
| - `Images/` — 72 files |
|
|
| 📝 Landmark annotations, visualization figures and the benchmark plan files live in 🔥[MedVision](https://huggingface.co/datasets/YongchengYAO/MedVision)🔥, where you can load the complete images and annotations from dataset configs. |
|
|
|
|
| ## Relation to the source dataset |
|
|
| | | | |
| | --- | --- | |
| | In the source | 72 T1-weighted MR scans (32 SNSX + 40 LHSCPD), 32 anatomical fiducials each | |
| | Excluded here | nothing — this is a complete mirror | |
| | **In this repo** | **72 `Images`** | |
|
|
| **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, 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](#preprocessing) below for exactly what was changed. |
|
|
|
|
| ## Preprocessing |
|
|
| - Images converted to 3D volumes in `nii.gz` format and standardized to RAS+ orientation. |
|
|
| - The 32 ground-truth fiducials per case were parsed from the `.fcsv` files (`# CoordinateSystem = 0`, i.e. RAS world-mm) and converted to 0-based voxel indices in the RAS+ volume, then saved as JSON. |
|
|
| - One T1w volume is kept per subject (32 SNSX + 40 LHSCPD = 72 cases). |
|
|
|
|
| ## Landmarks |
|
|
| ```python |
| landmarks_map = { |
| "P1": "anterior commissure", |
| "P2": "posterior commissure", |
| "P3": "infracollicular sulcus", |
| "P4": "pontomesencephalic junction", |
| "P5": "superior interpeduncular fossa", |
| "P6": "right superior lateral mesencephalic sulcus", |
| "P7": "left superior lateral mesencephalic sulcus", |
| "P8": "right inferior lateral mesencephalic sulcus", |
| "P9": "left inferior lateral mesencephalic sulcus", |
| "P10": "culmen", |
| "P11": "intermammillary sulcus", |
| "P12": "right mammillary body", |
| "P13": "left mammillary body", |
| "P14": "pineal gland", |
| "P15": "right lateral ventricle at anterior commissure", |
| "P16": "left lateral ventricle at anterior commissure", |
| "P17": "right lateral ventricle at posterior commissure", |
| "P18": "left lateral ventricle at posterior commissure", |
| "P19": "genu of the corpus callosum", |
| "P20": "splenium of the corpus callosum", |
| "P21": "right anterolateral temporal horn", |
| "P22": "left anterolateral temporal horn", |
| "P23": "right superior anteromedial temporal horn", |
| "P24": "left superior anteromedial temporal horn", |
| "P25": "right inferior anteromedial temporal horn", |
| "P26": "left inferior anteromedial temporal horn", |
| "P27": "right indusium griseum origin", |
| "P28": "left indusium griseum origin", |
| "P29": "right ventral occipital horn", |
| "P30": "left ventral occipital horn", |
| "P31": "right olfactory sulcal fundus", |
| "P32": "left olfactory sulcal fundus" |
| } |
| ``` |
|
|
|
|
| ## News |
| - [25 Jul, 2026] Initial release. This dataset is integrated into 🔥[MedVision](https://huggingface.co/datasets/YongchengYAO/MedVision)🔥, where you can use these config names to load data in python: |
|
|
| - `AFIDs_BiometricsFromLandmarks_Task01_Axial_Test` |
| - `AFIDs_BiometricsFromLandmarks_Task01_Axial_Train` |
| - `AFIDs_BiometricsFromLandmarks_Task01_Sagittal_Test` |
| - `AFIDs_BiometricsFromLandmarks_Task01_Sagittal_Train` |
|
|
|
|
| ## Data Usage Agreement |
| By using the dataset, you agree to the terms as follow. |
| - You must comply with the original `CC BY 4.0` license terms of the source dataset. |
| - You are recommended to refer to the source of this dataset in any publication: `https://huggingface.co/datasets/YongchengYAO/AFIDs-Lite` |
| - You must cite the original publication(s): |
| - https://doi.org/10.1038/s41597-024-04259-z |
|
|
|
|
| ## Official Release |
| For more information, please go to the official site: https://github.com/afids/afids-data |
|
|
|
|
| ## Download from Huggingface |
| ```python |
| # python |
| from huggingface_hub import snapshot_download |
| snapshot_download(repo_id="YongchengYAO/AFIDs-Lite", repo_type='dataset', local_dir="/your/local/folder") |
| ``` |
|
|
|
|
