Original codes and sample data from Kim et al. 2023, Neuron, "Whole-brain mapping of effective connectivity by fMRI with cortex-wide patterned optogenetics" (In press). The procedure described here is for generating subject-specific optogenetic stimulus pattern based on Allen mouse brain atlas (https://atlas.brain-map.org/), by coregistration between the Atlas, brain structural MR image and optical fluorescence image from a mouse. The generated patterns are transferred to a digital micromirror device (DMD) and then projected onto a thinned-skull-prepared mouse brain.
Steps to reproduce
Described in Readme.docx