I am trying to figure out what exactly the "transformation parameters" output by mcflirt represent.
For example, if I run:
mcflirt -in a.nii -out -plots
I get:
a_mcf.nii.gz <- motion corrected image
a_mcf.par <- "transformation parameters"
a_mcf.mat/MAT_0000 <- transformation matrices
a_mcf.mat/MAT_0001
...
The MAT_#### files are transformation matrices, where the fourth column represents the translation portion of the transformation. The transformation matrix for the first volume my example is:
0.999600 0.012941 0.025167 -2.545517
-0.014019 0.998969 0.043174 -1.139777
-0.024583 -0.043510 0.998750 6.326336
0.000000 0.000000 0.000000 1.000000
The rows of the 'a_mcf.par' file each store six numbers. I can't find any description from FSL about what these numbers actually represent, but I am guessing that 3 of these numbers store information about rotation, and three store information about translation. The "transformation parameters" output for the first volume in my example are:
0.0432012 -0.0251699 0.0129451 0.0363291 -0.18679 -0.216405
What do these six numbers represent, what are they measured relative to, and what *units* are they in? If the final three numbers in the motion parameters are related to translation, then why are they so different from the fourth column of the transformation matrix? How are the transformation matrix and transformation parameters related?
I've found other users with similar questions and no answer. It would be great if the contents of the "transformation parameters" files could be explained (ideally inside the mcflirt documentation and in the output of 'mcflirt -help').
Thanks
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