Hello,

Thank you for replying. Once the landmarks are detected and the matrices are saved, I am attempting the following:

To figure out the translation that is needed to be applied to shift the origin to the AC: convert the AC voxel location to coordinates in mm (by multiplying with the first three rows and columns of the header matrix) and then subtract from the original images' translation (the last column of the header matrix).

However, I am unsure of how to proceed with calculating the rotations. I tried deconstructing the header matrix into components but the rotation values do not look reasonable.

Here is the FSL matrix that I have:
-0.9995 -0.0116 0.0291 189.5262
0.0093 -0.9969 -0.0776 273.5740
-0.030 0.0773 -0.9965 262.7300
0 0 0 1

I used the spm_imatrix function (from SPM) to deconstruct it into translations and rotations:
translations = 189.5262, 273.5740, 262.7300 (x, y, z)
rotations = -3.0638 0.0292 -0.0116 (pitch, roll, yaw (the pitch value in radians is too high!)

The detected AC and PC locations are: 96.8, 141.8, 152.1 and 96.9, 118.3 152.1

To shift the origin to the AC, translation = -matrix(1:3,1:3)*AC_location - matrix(1:3,4)
which gives me 7.08, 11.29, and 9.5 mm shift in the right, forward, and up directions (seems reasonable; using these values does bring the origin to AC)

How can I go about calculating the rotations then to line up the PC? I apologize if this is trivial and/or if I am meandering down an overtly complicated path for no reason due to my limited understanding in this area.


Look forward to your thoughts

Warm Regards
Pravesh

Originally posted by Babak Ardekani: