~/path/to/acpcdetect -M -o <output/folder/acpc.nii> -i <input/folder/t1_Crop_1.nii>
The -M option causes the origin to be placed at the midpoint between the anterior commissure and posterior commissure.
The images are corrected for any bias field to provide consistent representations of uniform matter types. This step is done using the ANTs (Advanced Normalization Toolkit) program (version x downloaded from https://github.com/stnava/ANTs.git).