Dear Jesper,
I checked out fsl 5.0.9 and indeed it does output the .eddy_movement_rms file. Thank you for the clarifications.
Would this http://www.mathworks.com/matlabcentral/fileexchange/30804-make-fsl-compatible-transformation-matrix be a good way to obtain back the tranform mat file from the motion parameters? How about the eddy transformations? Finally, what does the .eddy_movement_rms file actually contain? Is it the absolute and relative mean displacement of eddy corrected image with respect to the motion corrected image?
Best,
--
Maria
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