ACPC alignment

This page describes how to align a T1-weighted anatomical volume into AC-PC space, providing a common orientation for visualizing the brain. AC (anterior commissure) and PC (posterior commissure) are 2 anatomical landmarks in the brain. For a brain that has been AC-PC aligned, the AC and PC are in the same axial plane.

http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Anatomical-Processing

The mrAnatAverageAcPcNifti function is used to perform this step. This function: (a) Aligns the T1-weighted scans to the first scan (if more than 1 T1-weighted scan is provided) (b) Reslices each scan to 1mm isotropic voxels (c) Averages the scans (d) Saves out the averaged resliced acpc'd nifti file.

we use the command

     mrAnatAverageAcPcNifti(fileNameList, outFileName)

where `fileNameList` is a cell array of T1w volumes and `outFileName` is something like 't1.nii.gz'. For Example

     mrAnatAverageAcPcNifti({'t1.1.nii.gz','t1.2.nii.gz'},'t1.ave.nii.gz')

will average the two t1s and then save the averaged ac-pc aligned nifti as t1.ave.nii.gz

When you run the line of code in MATLAB A GUI will launch for you to select the landmarks.

In the GUI: - Place cursor on the AC > Click "Set AC"

The anterior commissure is just below the anterior end of the fornix and should be relatively easy to see on the mid-sagittal slice. In the axial plane you can also see the white matter bundle splitting the basal ganglia on each side (just above the horizontal red line).

- Place cursor on the PC > Click "Set PC"

The posterior commissure is below and posterior to the thalamus and above the midbrain. In this sagittal slice you can easily see the stripe of white matter extending from the cerebellum anteriorly to the third ventricle.

- Place cursor on the mid-sagittal slice

 (making sure to choose a superior point on the sagittal slice, this helps the algorithm)

press finish. When the code is done aligning and averaging your anatomies you should get a reference image to look at to see how the averaging went.