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DOC: Add notes on processing level to outputs.rst
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effigies committed Nov 14, 2023
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Expand Up @@ -62,6 +62,28 @@ This layout, now the default, may be explicitly specified with the
For compatibility with versions of fMRIPrep prior to 21.0, the
`legacy layout`_ is available via ``--output-layout legacy``.

Processing level
----------------
As of version 23.2.0, fMRIPrep supports three levels of derivatives:

* ``--level minimal``: This processing mode aims to produce the smallest
working directory and output dataset possible, while enabling all further
processing results to be deterministically generated. Most components of
the `visual reports`_ can be generated at this level, so the quality of
preprocessing can be assessed. Because no resampling is done, confounds
and carpetplots will be missing from the reports.
* ``--level resampling``: This processing mode aims to produce additional
derivatives that enable third-party resampling, resampling BOLD series
in the working directory as needed, but these are not saved to the output
directory.
The ``--me-output-echos`` flag will be enabled at this level, in which
case the individual echos will be saved to the working directory after
slice-timing correction, head-motion correction, and susceptibility
distortion correction.
* ``--level full``: This processing mode aims to produce all derivatives
that have previously been a part of the fMRIPrep output dataset.
This is the default processing level.

Visual Reports
--------------
*fMRIPrep* outputs summary reports, written to ``<output dir>/fmriprep/sub-<subject_label>.html``.
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