Fmriprep smoothing option

fmriprep
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#1

Hi all,

Is there a way to specify spatial smoothing for fmriprep? Or is it better to perform it on the *bold_space-MNI152NLin2009cAsym_preproc.nii.gz files afterwards?

Also, am I correct in thinking that slice timing correction is not performed? (it’s labelled as future on github) Is there a way to do this before using fmriprep?

Thanks.


#2

Not currently, but we could add this feature as an option. Depending on the analysis different types of smoothing are required.

This is how we intended things to work. You can also perform smoothing on first level contrast maps, jsut before runnign group level.

You are correct - we are working on it!


#3

Therefore, what is the current best option to conduct slice timing correction together with fmriprep ?


#4

The best option is to help us implement it :slight_smile: https://github.com/poldracklab/fmriprep/issues/27

Otherwise, I would perform the slice time correction before feeding the files to FMRIPREP.


#5

That’s what I’ve been doing, slice time correct first using SPM12, then feed into fmriprep, then smoothing in SPM12.
Prelim results looks much more robust than the typical SPM preproc pipeline. Well worth the effort.
@ChrisGorgolewski Thank you for the software. Look forward to future updates!


#6

Slice timing correction has already been added according to https://github.com/poldracklab/fmriprep/pull/415 ?


#7

Yes - it’s in current master. Will be part of the next release.


#8

Thank you very much for really quick update. I’d like to decide which version to use, could you let me know the rough estimate when the next release will come?


#9

Most likely this week.


#10

Thank you very much! I’m looking forward to seeing the new release.