AutoAFIDs: BIDS App for landmark detection, QC, stereotactic targeting and brain charting

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Brain landmark localization is an important step in many neuroimaging and clinical workflows. For instance, identifying salient regions like the anterior (AC) and posterior commissure (PC) is common during brain alignment [1], and the AC-PC line is used as a reference during stereotactic targeting [2].
We extended the search for salient brain regions by creating [3] and validating [4] an open-access protocol for annotating 32 landmarks, called anatomical fiducials (AFIDs). However, manual localization is time intensive, making automation necessary for application in large-scale datasets and clinical use.
In this work, we introduce AutoAFIDs (github.com/afids), a BIDS App for automatic landmark detection using deep learning. We demonstrate its broad utility in three downstream applications: 1) image registration, 2) stereotactic targeting and 3) brain charting.