Annotations of Electrodes (DataID: 4958)

Method

The positions of electrodes of the electrocorticography (ECoG) for marmosets are normalized to the standard space, which is defined using the standard brain, BMA 2019 Ex vivo, in Brain/MINDS data portal.

This normalization consists of two steps: 1. electrode identification on the individual in vivo MRI (subject space) and 2. registration to the averaged ex vivo MRI (standard space). Here, we explain these two steps.

1. Electrode identification on the subject space

We obtain a computed tomography (CT) scan image of individual marmoset after an electrode implantation, and an in vivo T2 weighted magnetic resonance imaging (MRI) for the same individual marmoset before surgery. The CT image is manually aligned to the in vivo MRI space by rigid transformation using AFNI software (Cox, 1996). The electrodes are manually segmented from the CT images using 3D Slicer (Fedorov et al., 2012) to eliminate non-electrode regions and numbering the electrodes.

2. Registration to the standard space

The in vivo individual MRI (subject space) is registered to the in vivo average MRI data of marmosets by free-form deformation using ANTs software (Avants et al, 2011). The in vivo averaged MRI data is also registered to the standard space defined by BMA 2019 Ex vivo using ANTs software. Then, we map the segmented electrode on the subject space to those on the standard space based on these registrations. Finally we determine a nearest voxel of each electrode on the standard brain using a nearest neighbor method, and annotate a cortical region of the voxel to the electrode.