Brain age prediction of healthy subjects on anatomic MRI with deep learning: going beyond with an "explainable AI" mindset

Abstract

Objectives: Define a clinically usable preprocessing pipeline for MRI data. Predict brain age using various machine learning and deep learning algorithms. Define Caveat against common machine learning traps. Data and Methods: We used 1597 open-access T1 weighted MRI from 24 hospitals. Preprocessing consisted in applying: N4 bias field correction, registration to MNI152 space, white and grey stripe intensity normalization, skull stripping and brain tissue segmentation. Prediction of brain age was done with growing complexity of data input (histograms, grey matter from segmented MRI, raw data) and models for training (linear models, non linear model such as gradient boosting over decision trees, and 2D and 3D convolutional neural networks). Work on interpretability consisted in (i) proceeding on basic data visualization like correlations maps between age and voxels value, and generating (ii) weights maps of simpler models, (iii) heatmap from CNNs model with occlusion method. Results: Processing time seemed feasible in a radiological workflow: 5 min for one 3D T1 MRI. We found a significant correlation between age and gray matter volume with a correlation r = -0.74. Our best model obtained a mean absolute error of 3.60 years, with fine tuned convolution neural network (CNN) pretrained on ImageNet. We carefully analyzed and interpreted the center effect. Our work on interpretability on simpler models permitted to observe heterogeneity of prediction depending on brain regions known for being involved in ageing (grey matter, ventricles). Occlusion method of CNN showed the importance of Insula and deep grey matter (thalami, caudate nuclei) in predictions. Conclusions: Predicting the brain age using deep learning could be a standardized metric usable in daily neuroradiological reports. An explainable algorithm gives more confidence and acceptability for its use in practice. More clinical studies using this new quantitative biomarker in neurological diseases will show how to use it at its best.

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