Brain extraction and CSF segmentation on T1 MRI
Three-label segmentation (parenchyma, ventricles, internal CSF) on T1 brain MRI across axial, sagittal and coronal series.
A neuroimaging vendor was refining its brain-extraction (BET) pipeline and needed manual ground truth on T1 MRI across multiple orientations, with strict rules on which structures belong to parenchyma, ventricles and internal CSF.
Segment parenchyma (hemispheres, cerebellum, brainstem, hypothalamus) excluding ventricles, skull, eyeballs, optical nerves, choroid plexus, pituitary and longitudinal fissure; segment lateral, 3rd and 4th ventricles; and label as CSF only the areas surrounded by parenchyma (cisterns, sylvian fissures).
Radiologists worked on the client's segmentation tool with per-orientation reference cases from an expert neuroradiologist. Guidelines explicitly excluded the external edge CSF and enforced consistent handling of borderline structures across axial, sagittal and coronal acquisitions.
The client received orientation-agnostic ground truth compatible with its BET pipeline, with clean separation of parenchyma, ventricles and internal CSF across a heterogeneous set of T1 series.