Merge branch 'main' of https://huggingface.co/datasets/cdoswald/SPIDER

README.md

@@ -9,7 +9,7 @@ tags:
 - segmentation
 ---
 
-# Dataset Card for Spine Segmentation: Discs, Vertebrae and Spinal Canal (SPIDER)
+# Spine Segmentation: Discs, Vertebrae and Spinal Canal (SPIDER)
 
 The SPIDER dataset contains (human) lumbar spine magnetic resonance images (MRI) and segmentation masks described in the following paper:
 
@@ -28,7 +28,42 @@ Original data are available on [Zenodo](https://zenodo.org/records/8009680). Mor
   <figcaption>Example MRI scan with segmentation masks</figcaption>
 </figure>
 
-## Getting Started
+# Dataset Description
+
+- **Paper:** [Lumbar spine segmentation in MR images: a dataset and a public benchmark](https://www.nature.com/articles/s41597-024-03090-w) 
+- **Repository:** [Zenodo](https://zenodo.org/records/8009680)
+- **Grand Challenge:** [SPIDER Grand Challenge](https://spider.grand-challenge.org/)
+
+# Table of Contents (TOC)
+
+1. [Getting Started](https://huggingface.co/datasets/cdoswald/SPIDER#getting-started)
+   
+2. [Dataset Summary](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+3. [Data Modifications](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+4. [Dataset Structure](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+    - [Data Instances](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+    - [Data Format/Fields](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+    - [Data Splits](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+5. [Image Resolution](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+
+6. [Additional Information](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+    
+    - [License](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+    - [Citation](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+   
+    - [Disclaimer](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+
+
+<br>
+
+# Getting Started
 
 First, you will need to install the following dependencies:
 
@@ -40,24 +75,13 @@ Then you can load the SPIDER dataset as follows:
 
 ```python
 from datasets import load_dataset
-
 dataset = load_dataset("cdoswald/SPIDER, name="default", trust_remote_code=True)
 ```
 
 More detailed examples for [loading](tutorials/load_data.ipynb) the dataset with different configurations 
 and using the dataset for [segmentation tasks](tutorials/segment_anything.ipynb) are provided in the [tutorials](tutorials) folder.
 
-## Table of Contents
-
-(Placeholder--to be filled in at end of project)
-
-## Dataset Description
-
-- **Paper:** [Lumbar spine segmentation in MR images: a dataset and a public benchmark](https://www.nature.com/articles/s41597-024-03090-w) 
-- **Repository:** [Zenodo](https://zenodo.org/records/8009680)
-- **Grand Challenge:** [SPIDER Grand Challenge](https://spider.grand-challenge.org/)
-
-### Dataset Summary
+# Dataset Summary
 
 The dataset includes 447 sagittal T1 and T2 MRI series collected from 218 patients across four hospitals.
 Segmentation masks indicating the vertebrae, intervertebral discs (IVDs), and spinal canal are also included.
@@ -67,7 +91,7 @@ In addition to MR images and segmentation masks, additional metadata (e.g., scan
 patient characteristics (biological sex and age, when available), and radiological gradings indicating specific degenerative
 changes can be loaded with the corresponding image data.
 
-### Modifications to Original Data
+# Data Modifications
 
 This version of the SPIDER dataset (i.e., available through the HuggingFace `datasets` library) differs from the original 
 data available on [Zenodo](https://zenodo.org/records/8009680) in two key ways:
@@ -87,8 +111,7 @@ and 39 (15%) studies for the SPIDER Grand Challenge [hidden test set](https://sp
 their models to the SPIDER Grand Challenge, the original 218 studies that comprised the public training/validation set were further partitioned using a 60%/20%/20% split. The original split
 for each study (i.e., training or validation set) is recorded in the `OrigSubset` variable in the study's linked metadata.
 
-
-## Dataset Structure
+# Dataset Structure
 
 ### Data Instances
 
@@ -160,19 +183,19 @@ The dataset is split as follows:
 
 - Training set:
 	- 149 unique patients
-	- 304 images
+	- 304 total images
 		- T1: 133 images
 		- T2: 145 images
 		- T2-SPACE: 26 images
 - Validation set:
 	- 37 unique patients
-	- 75 images
+	- 75 total images
 		- T1: 34 images
 		- T2: 34 images
 		- T2-SPACE: 7 images
 - Test set:
 	- 32 unique patients
-	- 68 images
+	- 68 total images
 		- T1: 29 images
 		- T2: 31 images
 		- T2-SPACE: 8 images
@@ -181,7 +204,7 @@ An additional hidden test set provided by the paper authors
 (i.e., not available via HuggingFace) is available on the 
 [SPIDER Grand Challenge](https://spider.grand-challenge.org/spiders-challenge/).
 
-## Image Resolution
+# Image Resolution
 
 > Standard sagittal T1 and T2 image resolution ranges from 3.3 x 0.33 x 0.33 mm to 4.8 x 0.90 x 0.90 mm. 
 > Sagittal T2 SPACE sequence images had a near isotropic spatial resolution with a voxel size of 0.90 x 0.47 x 0.47 mm.
@@ -192,7 +215,7 @@ for compatibility with the HuggingFace `datasets` library. If you want to use th
 load the original images from the local cache indicated in each example's `image_path` and `mask_path` features.
 See the data loading [tutorial](tutorials/load_data.ipynb) for more information.
 
-## Additional Information
+# Additional Information
 
 ### License