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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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--output-spaces MNI152NLin6Asym for Schaefer's atlas? #2618

Closed GerardYu closed 2 years ago

GerardYu commented 2 years ago

i intend to use the schaefers atlas from nilearn (datasets.fetch_atlas_schaefer_2018(200)) to construct my FC matrices. I see that the downloaded atlas template has the filename of "Schaefer2018_200Parcels_7Networks_order_FSLMNI152_1mm.nii.gz" — suggesting that this template is in the FSL MNI space.

does this mean i should run my fmriprep with the --output-spaces MNI152NLin6Asym option?

effigies commented 2 years ago

I don't know what specific template they use. If you're not wedded to nilearn's parcellation, you can find Schaefer parcellations in both MNI152NLin6Asym and MNI152NLin2009cAsym templates: https://www.templateflow.org/browse/

oesteban commented 2 years ago

AFAICT, nilearn's atlas is defined on MNI152NLin6Asym. However, best practice would be downloading it from TemplateFlow, as the orientation of the NIfTI files is matched with that of the template fMRIPrep is using. If I'm not wrong, I think we also resampled the Schaefer atlas into MNI152NLin2009cAsym, so either way you will be able to use the atlas.