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

README.md

@@ -54,26 +54,27 @@ In addition to the information in this README, several detailed tutorials are pr
    
 2. [Dataset Summary](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
    
-3. [Data Modifications](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+3. [Data Modifications](https://huggingface.co/datasets/cdoswald/SPIDER#data-modifications)
    
-4. [Dataset Structure](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+4. [Dataset Structure](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-structure)
    
-    - [Data Instances](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+    - [Data Instances](https://huggingface.co/datasets/cdoswald/SPIDER#data-instances)
    
-    - [Data Format/Fields](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+    - [Data Schema](https://huggingface.co/datasets/cdoswald/SPIDER#data-schema)
    
-    - [Data Splits](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+    - [Data Splits](https://huggingface.co/datasets/cdoswald/SPIDER#data-splits)
    
-5. [Image Resolution](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+5. [Image Resolution](https://huggingface.co/datasets/cdoswald/SPIDER#image-resolution)
 
-6. [Additional Information](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+6. [Additional Information](https://huggingface.co/datasets/cdoswald/SPIDER#additional-information)
     
-    - [License](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+    - [License](https://huggingface.co/datasets/cdoswald/SPIDER#license)
    
-    - [Citation](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
+    - [Citation](https://huggingface.co/datasets/cdoswald/SPIDER#citation)
    
-    - [Disclaimer](https://huggingface.co/datasets/cdoswald/SPIDER#dataset-summary)
-
+    - [Disclaimer](https://huggingface.co/datasets/cdoswald/SPIDER#disclaimer)
+  
+    - [Known Issues/Bugs](https://huggingface.co/datasets/cdoswald/SPIDER#known-issuesbugs)
 
 <br>
 
@@ -130,7 +131,7 @@ for each study (i.e., training or validation set) is recorded in the `OrigSubset
 
 There are 447 images and corresponding segmentation masks for 218 unique patients.
 
-### Data Format/Fields
+### Data Schema
 
 The format for each generated data instance is as follows:
 
@@ -140,13 +141,21 @@ The format for each generated data instance is as follows:
 
 3. **image**: a 3-dimensional volumetric array (height, width, depth) of values indicating pixel intensities of MRI scan
 
-4. **mask**: a 3-dimensional volumetric array (height, width, depth) of values indicating manually segmented feature of interest
+4. **mask**: a 3-dimensional volumetric array (height, width, depth) of values indicating the following segmented anatomical feature(s):
+
+    - 0 = background
+    - 1-25 = vertebrae (numbered from the bottom, i.e., L5 = 1)
+    - 100 = spinal canal
+    - 101-125 = partially visible vertebrae
+    - 201-225 = intervertebral discs (numbered from the bottom, i.e., L5/S1 = 201)
+
+    See the [SPIDER Grand Challenge](https://grand-challenge.org/algorithms/spider-baseline-iis/) documentation for more details.
 
-5. **image_path**: path to the local cache containing the original (non-rescaled and non-resized) MRI image
+6. **image_path**: path to the local cache containing the original (non-rescaled and non-resized) MRI image
 
-6. **mask_path**: path to the local cache containing the original (non-rescaled and non-resized) segementation mask
+7. **mask_path**: path to the local cache containing the original (non-rescaled and non-resized) segementation mask
 
-7. **metadata**: a dictionary of metadata of image, patient, and scanner characteristics:
+8. **metadata**: a dictionary of metadata of image, patient, and scanner characteristics:
 
     - number of vertebrae
     - number of discs
@@ -197,21 +206,21 @@ The dataset is split as follows:
 - Training set:
 	- 149 unique patients
 	- 304 total images
-		- T1: 133 images
-		- T2: 145 images
-		- T2-SPACE: 26 images
+		- Sagittal T1: 133 images
+		- Sagittal T2: 145 images
+		- Sagittal T2-SPACE: 26 images
 - Validation set:
 	- 37 unique patients
 	- 75 total images
-		- T1: 34 images
-		- T2: 34 images
-		- T2-SPACE: 7 images
+		- Sagittal T1: 34 images
+		- Sagittal T2: 34 images
+		- Sagittal T2-SPACE: 7 images
 - Test set:
 	- 32 unique patients
 	- 68 total images
-		- T1: 29 images
-		- T2: 31 images
-		- T2-SPACE: 8 images
+		- Sagittal T1: 29 images
+		- Sagittal T2: 31 images
+		- Sagittal T2-SPACE: 8 images
 
 An additional hidden test set provided by the paper authors
 (i.e., not available via HuggingFace) is available on the 
@@ -226,7 +235,7 @@ An additional hidden test set provided by the paper authors
 Note that all images are rescaled to have pixel intensities in the range `[0, 255]` (i.e., unsigned 8-bit integers)
 for compatibility with the HuggingFace `datasets` library. If you want to use the original resolution, you can
 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.
+See the [tutorial](tutorials/load_data.ipynb) for more information.
 
 # Additional Information
 
@@ -241,4 +250,10 @@ The dataset is published under a CC-BY 4.0 license: https://creativecommons.org/
 ### Disclaimer
 
 I am not affiliated in any way with the aforementioned paper, researchers, or organizations. Please validate any findings using this curated dataset
-against the original data provided by the researchers on [Zenodo](https://zenodo.org/records/8009680).)
+against the original data provided by the researchers on [Zenodo](https://zenodo.org/records/8009680).)
+
+### Known Issues/Bugs
+
+1. Serializing data into Apache Arrow format is required to make the dataset available via HuggingFace's `datasets` library. However, it introduces some segmentation
+mask integer values that do not map exactly to a defined [anatomical feature category](https://grand-challenge.org/algorithms/spider-baseline-iis/).
+See the data loading [tutorial](tutorials/load_data.ipynb) for more information and temporary work-arounds.