Dear Jesper,
Thank you for your reply. Indeed I have included in this matrix the rotations and the translations. I am actually using this method to get the transformation matrix: http://www.mathworks.com/matlabcentral/fileexchange/30804-make-fsl-compatible-transformation-matrix/content/makeFslXfmMatrix.m. Could you confirm that the rotation matrices are correct and that the rotations are applied as per: Rx*Ry*Rz?
Furthermore, regarding the rotation-center for eddy - are you referring here to the center of gravity that can be received from fslstats? I tried to add those values as extra translations to the transformation matrices but I get a result that is translated so much that it becomes out of focus. How should I use this information?
If I don't do anything about the center of rotation and just apply my transformation matrices (assuming they are correctly generated as per the script mentioned above) I get a set of volumes that still has motion correction.
Best regards,
Maria
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