fMRIPrep description of methodology

Hi all,

I am currently trying to write the methodology of my pipeline in fMRIPrep but I seem to have a slight issue with the automatically generated description of the fMRIpreprocessing.

In the original analysis of fMRIprep I had included the ICA-AROMA option (version 21.0.0) but I opted out of using it in my analysis and instead I used the uncleaned preprocessed fMRI output.

In the wording of what analysis took place though, after the ICA-AROMA description, there is this output:

All resamplings can be performed with a single interpolation step by composing all the pertinent transformations (i.e. head-motion transform matrices, susceptibility distortion correction when available, and co-registrations to anatomical and output spaces). Gridded (volumetric) resamplings were performed using antsApplyTransforms (ANTs), configured with Lanczos interpolation to minimize the smoothing effects of other kernels (Lanczos 1964). Non-gridded (surface) resamplings were performed using mri_vol2surf (FreeSurfer).

Would this be relevant in the description of my analysis? In my case I am only using the WM and CSF nuiance regressors but I was not sure what the resamplings are reffering to.



Hi George,

There are several resampling steps that happen in fMRIPrep. Even if you aren’t using AROMA outputs, your BOLD images have to aligned to the T1 image, and then additionally aligned to whatever output space you specify (which is informed by the subjects T1 image). There are also warps from motion correction and susceptibility distortion correction. Short answer: this part of the write up is still probably relevant for you. If you are not using data (CIFTI/fsaverage output space) then maybe you can remove the last sentence.


Thank you very much for your clarification.
Have a nice weekend!

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