This was a question I received by E-mail:

I was wondering if you knew where the transformation matrix of
original view -> ACPC view is written down? (what exactly is done with the
coordinates of the AC, PC, and 2 midpoints. i tried figuring it out on my
own, but want to confirm the calculation of my matrix with AFNI's) I tried
looking through the documentation, but have been unsuccessful in finding
the rotation matrix.

This was my answer to the "where is the matrix? " part (I dodged the "what exactly is done with the coordinates of the AC, PC ...? " part)

The transformation matrix (3x3) + shift vector are stored in the header field WARP_DATA of the PREFIX_HERE+acpc.HEAD file. You can get the values of the WARP_DATA field using a text editor or with the convenient program 3dAttribute.

Example: 3dAttribute WARP_DATA PREFIX_HERE+acpc.HEAD

WARP_DATA contains 30 values for the acpc aligned data and 360 for the +tlrc data. This sounds terrifying but it isn't. This field is quite extensively documented in the file README.attributes found here: [afni.nimh.nih.gov]

( lots of other README files and Postscript documentation for many of AFNI's programs are found here: [afni.nimh.nih.gov] )

Make sure you read the section labeled "Warping Attributes" till the end. The acpc story does not end until the very last paragraph.

If you are adventurous enough to read the C code, the program Vecwarp.c is a great place to start. You might also find the programs adwarp, 3dWarp and Vecwarp useful.



cheers,
-ziad