FSL 1st level turning off preprocessing steps

Hi,

I am trying to generate my template fsf files for fsl. I’m using fmriprep for the preprocessing.

I watched this helpful video https://www.youtube.com/watch?v=U3tG7JMEf7M which clarified what I need to do to make the higher level analyses work. However, when I run the 1st level analyses should I turn off these settings

  1. Mcflirt motion correction
  2. spatial smoothing
  3. high pass filtering

and then run the full analyses using the MNI standard brain in the registration?

Also, just to be sure, I should NOT use the “bold_space-MNI152NLin2009cAsym_preproc.nii.gz”
Nifti file produced by fmriprep for my 4d directory right? It should just be the raw functional file right?

We perform motion correction, but not smoothing or high-pass filtering.

(Note, however, that if you use aCompCor or tCompCor confounds, then you should also use the CosineXX confounds to perform high-pass filtering, as the CompCor components are calculated after high-pass filtering.)

No, you should use the preprocessed outputs, not the raw data.

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