fMRIPrep version 21.0.0 output

Hi All, In previous versions of fMRIPrep, when you specify bidsroot/derivatives as your output directory, two folders of ‘fmriprep’ and ‘freesurfer’ are created under derivatives, which will hold all the output files.

In the latest version of fMRIPrep (21.0.0), however, all the output will be placed directly under derivatives and not under a separate ‘fmriprep’ folder; ‘freesurfer’ will also be located under derivatives/sourcedata and not under a derivatives/freesurfer folder. Is there a reason for this change compared to the previous version? Things are a little messy under derivatives with this situation.

Please see the layout and legacy layout sections of: Outputs of fMRIPrep — fmriprep version documentation

The reason is to give users more control over the organization of the outputs instead of forcing a subdirectory. The old behavior is still achievable, if you prefer that.

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