The FreeSurfer subcortical “training set” is derived from manually labeled MRI scans of human brains, combined with statistical modeling to create probabilistic atlases. This process begins with expert neuroanatomists meticulously segmenting subcortical structures (e.g., hippocampus, amygdala, thalamus) in a large cohort of high-resolution MRI images. These manual annotations serve as the ground truth, defining the precise boundaries of each structure according to established anatomical guidelines. The labeled dataset typically includes scans from diverse populations to account for variations in age, sex, and pathology, ensuring the resulting models generalize well across different use cases. For example, datasets like the Alzheimer’s Disease Neuroimaging Initiative (ADNI) or healthy control cohorts are often used to capture a range of anatomical variability.
Once the manual segmentations are complete, the MRI scans undergo preprocessing to standardize the data. This includes steps like intensity normalization to correct scanner-specific brightness variations, skull stripping to remove non-brain tissue, and spatial alignment to a common coordinate system (e.g., MNI152 or Talairach space). The preprocessed scans and their corresponding labels are then used to build probabilistic atlases. These atlases encode spatial information—such as the likelihood of a voxel belonging to a specific subcortical structure—based on the distribution of manual labels across the training set. FreeSurfer’s algorithms use these atlases to inform Bayesian inference or machine learning models, which learn patterns of intensity and shape associated with each structure. For instance, the caudate nucleus might be modeled as a C-shaped region with specific intensity profiles relative to surrounding white matter.
The final training set is validated through iterative testing to ensure accuracy. Cross-validation techniques, such as splitting the dataset into training and testing subsets, help quantify segmentation performance metrics (e.g., Dice coefficients). Discrepancies between automated and manual segmentations are analyzed to refine the models, often by incorporating additional training data or adjusting feature weights. This cycle of training, validation, and refinement ensures the subcortical segmentation tools in FreeSurfer remain robust. Developers can extend these principles by integrating custom training data or modifying atlas parameters, making the framework adaptable to specialized research needs, such as pediatric neuroimaging or studies of neurodegenerative diseases.