Dear Jesper,
Thank you for the useful information! I am looking forward to see the plots. I have some smaller questions:
a. Are these eddy options still supported?:
1. considering that I lack reversed phase encoding direction acquisition, I'd like to use the --slm=linear option. Is fsl 5.0.7/5.0.8 still supporting this option? I get an error that suggest the option might not be supported.
2. I wanted to run eddy with --fwhm=10,0,0,0,0 as per http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/UsersGuide/#A--fwhm, just to see whether there is a difference between the motion correction obtained with --fwhm=0 (the default) and the suggested --fwhm=10,0,0,0,0. However, once again, I get an error that suggest the option might not be supported.
b. I am assuming that one would choose the number of iterations for eddy based on a convergence criterion. Is this the mss displayed for each iteration? If so, is it correct to say that the first series of mss values is related to motion and the second to eddy correction? What are values considered to be sufficient as a stopping criteria? In my case, the mss values from the 1st round of iterations slightly decrease from 3.1 to 2.224 in 5 iterations but for the 2nd round of iterations the total mss remains constant to 247.474. Just as a side remark: I believe that previously when I had run mcflirt before eddy I had gotten much lower total mss value for the 1st round of iterations, i.e., aprox. 0.7.
Best
--
Maria
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