Incorporating T2-Weighted Data in fMRIprep

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1

Hi,

If I want to use fMRIprep for structural preprocessing, and I only have T2-weighted data for some of the subjects, should I incorporate the T2-weighted data for those subjects, or should I keep it consistent for all subjects and not incorporate the T2-weighted data at all? Thanks!

2

I also want to add that the data I have does not include fieldmap data. Does this mean that B0 mapping cannot be performed? It isn’t mandatory, is it? How significantly would this affect the data quality?

3

Hi @ShuningW,

fMRIPrep requires T1w images. Subjects without them will not able to be processed. T2 images are only used to refine the pial surface in freesurfer and improve BOLD —> T1 registration. I would use the T2s if you have them.

Best,
Steven

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4

Regarding your lack of field maps, this means that your BOLD will be warped in places like the temporal and frontal lobes, which are particularly susceptible to distortions from magnetic field inhomogeneities. I don’t know your analysis goals so I can’t say how important that is to you.

Best,
Steven

5

I get it. Thank you so much!

Bests,
Shuning