Hello Freesurfer Forum,
We have a question about the M matrix, found in the .mgz file header.
We loaded an .mgz file into Matlab and took a look at the affine transform matrix M from the header:
M(1,:) = [-1 0 0 132.7486]; M(2,:) = [ 0 0 1 -105.7281]; M(3,:) = [ 0 -1 0 131.7424]; M(4,:) = [ 0 0 0 1 ];
Let's call these numbers:
M(1,:) = [ a 0 0 xt ]; M(2,:) = [ 0 0 c yt ]; M(3,:) = [ 0 b 0 zt ]; M(4,:) = [ 0 0 0 1 ];
We interpret a b and c as controlling rotation. xt yt zt govern translation. However, we cannot see how this matrix controls scaling.
We were expecting to see the following:
M(1,:) = [ xs 0 0 xt ]; M(2,:) = [ 0 ys 0 yt ]; M(3,:) = [ 0 0 zs zt ]; M(4,:) = [ 0 0 0 1 ];
...where xs yx zs control scaling. In our empirical matrix they do not seem to be serving that function. (xs appears to be used for rotation only, ys and zs are zero).
So the first question is: does the matrix control scaling, and if so, how?
The second question: Is the scaling built into the image, such that each voxel is 1mm by 1mm by 1mm? If so, how can the program tell when this is the case, and when it is not? Does ndim1 represent the number of voxels in that dimension, or the distance across that dimension in millimeters? Does ras_good_flag simply indicate that the image is in the proper orientation, or does it also indicate that each voxel in the image measures 1mm x 1mm x 1mm?
Thanks for your help.
Jerry Chen and Geoff Pope