fMRIprep won't ignore fieldmap

[nschneck]

I don’t know how this is happening. I’m running fmriprep with the --ignore fieldmaps option and I even deleted the fieldmaps from the input data. While fmriprep is running it says fieldmaps ignored. Nevertheless the final folders include the fieldmaps and the SDC? Any idea how or why this can happen and how to stop it from happening.

The only explanation I can think of is that I ran these initially with the fieldmaps and now I’ve copied over the freesurfer folders and I am running now without fieldmaps. Could that cause fmriprep to ignore the “ignore fieldmaps” conmand?

[effigies]

Could you provide a more detailed description of the problem? This in particular is unclear:

Nevertheless the final folders include the fieldmaps and the SDC?

A screenshot or a listing of the relevant file tree might be helpful.

The only explanation I can think of is that I ran these initially with the fieldmaps and now I’ve copied over the freesurfer folders and I am running now without fieldmaps.

If you’re reusing the output directory from a previous run, fMRIPrep will only overwrite files that it replaces. It’s probably best to use a clean output directory.

But again, without more detail, it’s hard to say what’s going on.