  Transfer learning has remarkably improved computer vision. These advances
also promise improvements in neuroimaging, where training set sizes are often
small. However, various difficulties arise in directly applying models
pretrained on natural images to radiologic images, such as MRIs. In particular,
a mismatch in the input space (2D images vs. 3D MRIs) restricts the direct
transfer of models, often forcing us to consider only a few MRI slices as
input. To this end, we leverage the 2D-Slice-CNN architecture of Gupta et al.
(2021), which embeds all the MRI slices with 2D encoders (neural networks that
take 2D image input) and combines them via permutation-invariant layers. With
the insight that the pretrained model can serve as the 2D encoder, we
initialize the 2D encoder with ImageNet pretrained weights that outperform
those initialized and trained from scratch on two neuroimaging tasks -- brain
age prediction on the UK Biobank dataset and Alzheimer's disease detection on
the ADNI dataset. Further, we improve the modeling capabilities of 2D-Slice
models by incorporating spatial information through position embeddings, which
can improve the performance in some cases.
