Hippocampus Segmentation Model

Purpose

This documentation describes our pre-trained model for segmentation of the left and right hippocampi from brain MRI scans. The model was trained on data from the ADNI dataset (for more information see the model card below). This data is publicly available via their website, but users must sign a Data Use Agreement in order to gain access. We do not provide access to the data. The following description assumes the user has their own dataset to evaluate/ retrain the model on.

Terms of use

Please note that this model is intended for research purposes only. You are responsible for the performance, the necessary testing, and if needed any regulatory clearance for any of the models produced by this toolbox.

Download

The hippocampus segmentation model can be downloaded from this release.

Connected components

It is possible to apply connected components as a post-processing step, although by default this is disabled. To enable, update the property largest_connected_component_foreground_classes of the Hippocampus class in InnerEye/ML/configs/segmentation/Hippocampus.py

Model Card

Model details

• Organisation: Biomedical Imaging Team at Microsoft Research, Cambridge UK.

• Model date: 5th July 2022.

• Model version: 0.1 . Currently only one version of the model has been released. We do not expect to update the model frequently.

• Model type: 3d UNET ensemble of 3d UNet. Training details are as described in this paper.

• Training details: 5 fold ensemble model. Trained on a subsection of the ADNI dataset (described in detail below)

• License: The model is released under MIT license as described here.

• Contact: innereyeinfo@microsoft.com.

Limitations

This model has been trained on a subset of the ADNI dataset. There have been various phases of ADNI spanning different time periods. In this Model Card we refer to the original, or ADNI 1, study. This dataset comprises scans and metadata from patients between the ages of 55-90 from 57 different sites across the US and Canada source. Therefore a major limitation of this model would be the ability to generalise to patients outside of this demographic. Another limitation is that The MRI protocol for ADNI1 (which was collected between 2004-2009) focused on imaging on 1.5T scanners source. Modern scanners may have higher field strengths and therefore different levels of contrast which could lead to different performance from the results we report.

The results of this model have not been validated by clinical experts. We expect the user to evaluate the result

Intended Uses

This model is for research purposes only. It is intended to be used for the task of segmenting hippocampi from brain MRI scans. Any other task is out of scope for this model.

About the data

The model was trained on 998 pairs of MRI segmentation + segmentation. The model was further validated on 127 pairs of images and tested on 125 pairs. A further 317 pairs were retained as a held-out test set for the final evaluation of the model, which is what we report performance on.

All of this data comes from the Alzheimer’s Disease Neuroimaging Initiative study link to website. The data is publicly available, but requires signing a Data Use Agreement before access is granted.

About the ground-truth segmentations

The segmentations were also downloaded from the ADNI dataset. They were created semi-automatically using software from Medtronic Surgical Navigation Technologies. Further information is available on the ADNI website.

Metrics

Note that due to the ADNI Data Usage Agreement we are only able to share aggregate-level metrics from our evaluation. Evaluation is performed on a held out test set of 252 pairs of MRI + segmentation pairs from the ADNI dataset.

Dice Score for Left and Right hippocampus respectively on a held-out test set of :

Structure	count	DiceNumeric_mean	DiceNumeric_std	DiceNumeric_min	DiceNumeric_max	HausdorffDistance_mm_mean	HausdorffDistance_mm_std	HausdorffDistance_mm_min	HausdorffDistance_mm_max	MeanDistance_mm_mean	MeanDistance_mm_std	MeanDistance_mm_min	MeanDistance_mm_max
hippocampus_L	252	0.918	0.022	0.819	0.953	2.206	0.812	1.206	6.964	0.168	0.054	0.096	0.399
hippocampus_R	252	0.918	0.024	0.816	0.954	2.185	0.706	1.206	4.966	0.168	0.055	0.094	0.433