Align images using Automatic Registration Toolbox acpcdetect (V2011-4-5, Website download https://www.nitrc.org/projects/art.)
We used the Automatic Registration Tool (ART) acpcdetect module to align the T1-weighted image so that the anterior commissure (AC) and posterior commissure (PC) lie along a horizontal plane with the mid-sagittal plant passing through each landmark. The module uses a rigid-body transformation for this alignment.
In the terminal bash command code that follows the input IMAGE is the t1.nii file from the previous step. The output is a T1 Nifti file with the anterior and posterior commissures aligned on the same horizontal plane. The -M option centers the origin midway between the anterior and posterior commissures.