Brain regions

Brain regions define which anatomical areas are included in outputs and statistics. They are also shown in atlas registration and can help during manual atlas adjustments.

Selected regions determine where quantification results are aggregated and reported.

Finding your brain regions

You can search for regions by name using the search bar. It filters the full list and shows only matching brain regions.

You can also click Preview to open an atlas viewer for the selected region.

Setup guidance

• Select regions relevant to your study question
• Keep selection focused to improve interpretability
• Choose regions that are covered by the images used for analysis

For 4x reference + detail projects, the analyzed detail field may cover only part of the brain slice, so region coverage should be checked against the detail images.

For high-res whole-slice projects, the analyzed image covers the full slice, so region coverage is usually limited by tissue quality, section position, and atlas registration rather than a separate detail field.

At least one brain region is required for a valid study setup.

Recommendations

• Start with your primary target regions
• Decide how detailed your final statistics should be before selecting many subregions
• Revisit brain region selection once data is uploaded and Results are available