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For now, I think I have found the problem! It explains why I had the issue with the motion tracker on or off. The cause was not the tracker itself but the way the function which was writing the output was implemented. It was messing up the sampling, slowing it down, since the output file had to be opened, data saved and written each time.
Now that I am only saving data at each timepoint and writing it only once at the very end, the issue seems to be gone.
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