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History of AFNI updates  

June 16, 2021 04:03PM
I haven't used FMRIprep, and don't know what those files look like.

Also, I could be mistaken, but I thought that FMRIprep by default uses AFNI's 3dvolreg for motion estimation. FMRIprep uses a lot of software tools across existing packages, and I think they picked AFNI's for default motion estimation, for example because of its high-rating when evaluating motion correction tools:
Oakes TR, Johnstone T, Ores Walsh KS, Greischar LL, Alexander AL, Fox AS, Davidson RJ (2005). Comparison of fMRI motion correction software tools. Neuroimage. 28(3):529-543. doi:10.1016/j.neuroimage.2005.05.058

Can you check that? I'm not sure what you processing you want done in FMRIprep and which in, but if that is the case, then it might just make sense to do that part in (which will also use 3dvolreg) rather than import with, say, this option:
-regress_motion_file FILE.1D  : use FILE.1D for motion parameters

                e.g. -regress_motion_file motion.1D

            Particularly if the user performs motion correction outside of
  , they may wish to specify a motion parameter file
            other than dfile_rall.1D (the default generated in the volreg

            Note: such files no longer need to be copied via -copy_files.

            If the motion file is in a remote directory, include the path,
            e.g. -regress_motion_file ../subject17/data/motion.1D .

Subject Author Posted

fMRIPrep motion files

MXD2019 June 16, 2021 03:24PM

Re: fMRIPrep motion files

ptaylor June 16, 2021 04:03PM

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