Hi FSL experts,
I am trying to run a PPI using the directions here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PPIHowToRun
When I am setting up the level 1 analysis for PPI in Feat, the data input is the filtered_func_data obtained from my prior level1 Feat for the standard activation analysis (for each run, for each subject). The instructions say:" If you are using the filtered_func from your GLM analysis as input, remember not to re-do any pre-processing steps such as BET, deleting volumes, or filtering."
Does that mean that I turn off *all* steps of prestats, also including: motion correction, slice timing correction, spatial smoothing and registration? Maybe the intuitive answer is yes, but I am not 100% sure when the filtered_func output was generated from the activation level1 feat.
For example here is where I am getting confused:
I ran MCFLIRT in the previous activation level1 feat, so I am assuming the filtered_func_data is already corrected for motion. Thus actual motion correction isn't needed here for the PPI level1 feat. However, when I don't include a motion correction option like MCFLIRT in the Pre-Stats tab of the Feat GUI, then I can no longer add motion parameters to my GLM in the Stats tab. Is there a way I can pull the motion parameters (Standard + Extended Motion Parameters) from the previous feat analysis to add them into this level1 GLM for the PPI?
Thanks,
Michelle
|