Are the motion parameters calculated in reference to the middle/median volume or the first volume?
My understanding is that by default MCFLIRT uses the middle (or median) volume as reference, but when I extract the 6 motion parameters from the ‘counfounds_timeseries.tsv’ file (as described here Using fMRIPrep motion confounds in FEAT's Stats first level) and plot them, it appears that they are calculated from the first volume.
The motion correction parameters are calculated with respect to the reference images created by fmriprep:
This workflow estimates a reference image for a BOLD series as follows: When T1-saturation effects (“dummy scans” or non-steady state volumes) are detected, they are averaged and used as reference due to their superior tissue contrast. Otherwise, a median of motion corrected subset of volumes is used.
