fMRIPrep Slice Time Correction Nipy

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1

Hi All,

I recently became aware of this blog post on the need to adjust my data due to slice time correction issues after fmriPrep if I use Nilearn for my level-1 analysis.

Is it sufficient to just subtract 1/2TR from the onset of my event matrices? I believe the answer is yes but would like to make sure I’m not missing anything.

Thanks,
Thomas Henning

2

Hi @NordicNarwhal,

You could also just specify the slice_time_ref parameter of nilearn.glm.first_level.FirstLevelModel - Nilearn.

Best,
Steven

3

I’m using Nltools to do my regression, so wanted to figure out if there was an easy way to make this change without having to rewrite significant parts of my workflow. Do you know if there is a way?

4

Sorry, I don’t use that toolbox, and also don’t know what code you are currently using, so I can’t help much at this point for that.

5

Is the relevant issue just that the onsets are shifted by 1/2TR? So that I just need to subtract 1/2TR to the onsets of all of my events before generating my design matrix and then I can run everything the same?

Update: This seems to be correct, as shown in this document: Slice timing correction in fMRIprep and linear modeling | Stanford Center for Reproducible Neuroscience