Hi Mark (and FSL community),
I wanted to reply to this (old) thread as I am experiencing the same issue. I used --dummy=4 in the fsl_motion_outliers command to remove the first 4 volumes. This is consistent with my entry in the FEAT GUI (and .fsf template for batch scripting as well).
For motion outliers, I am running the following command:
fsl_motion_outliers -i $FUNCFILE -o $DATADIR/motion_confound.txt -s $DATADIR/fd.txt -p $DATADIR/fd_plot.txt --fd --thresh=0.9 --dummy=4 -v
When I run this, the fd.txt document shows 328 timepoints (what I want). However, the outlier matrix (motion_confound.txt) shows 329 lines. I assume this causing the incompatibility within FEAT when I attempt to run the 1st level model, entering it in as an additional confound EV.
Is there a reason for the additional line? Any suggestion for a fix?
Thank you for help!
Best,
Erin
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