  A major challenge in stroke research and stroke recovery predictions is the
determination of a stroke lesion's extent and its impact on relevant brain
systems. Manual segmentation of stroke lesions from 3D magnetic resonance (MR)
imaging volumes, the current gold standard, is not only very time-consuming,
but its accuracy highly depends on the operator's experience. As a result,
there is a need for a fully automated segmentation method that can efficiently
and objectively measure lesion extent and the impact of each lesion to predict
impairment and recovery potential which might be beneficial for clinical,
translational, and research settings. We have implemented and tested a fully
automatic method for stroke lesion segmentation which was developed using eight
different 2D-model architectures trained via transfer learning (TL) and mixed
data approaches. Additionally, the final prediction was made using a novel
ensemble method involving stacking and agreement window. Our novel method was
evaluated in a novel in-house dataset containing 22 T1w brain MR images, which
were challenging in various perspectives, but mostly because they included T1w
MR images from the subacute (which typically less well defined T1 lesions) and
chronic stroke phase (which typically means well defined T1-lesions).
Cross-validation results indicate that our new method can efficiently and
automatically segment lesions fast and with high accuracy compared to ground
truth. In addition to segmentation, we provide lesion volume and weighted
lesion load of relevant brain systems based on the lesions' overlap with a
canonical structural motor system that stretches from the cortical motor region
to the lowest end of the brain stem.
