FSL 1st level analysis with fmriprep output


I am trying to perform first level analyses on fsl using the output from fmriprep. Which of the many output files that fmriprep provides should I use to register the subjects anatomical and functional scans? Very new to this so any advice will help.

Have a look at:

Thanks! However, I do not have nipype and figuring out this fitlins program seems like a lot of extra steps. I’m just looking for how to do this in fsl with fmriprep outputs.



Thank you for the links.
I’ve tried using these methods on my fmriprep pre-processed data, but I’m struggeling with adding the right regressors.
When adding them according to the above example I get an error running spm’s 1st level design.
Any ideas as to what might go wrong?

Is this related to Spm_mat_file in spm Level1Design ?

Indeed. Seems that the problem was solved.
Thank you.

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