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ENH: add segmentation documentation
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docs/usage.rst

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@@ -176,6 +176,22 @@ This feature has several intended use-cases:
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See also the ``--level`` flag, which can be used to control which derivatives are
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generated.
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Segmentation
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----------------
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*PETPrep* can segment the brain into different brain regions and extract time activity curves from these regions.
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The ``--seg`` flag selects the segmentation method to use.
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Available options are ``gtm`` (default) whole-brain segmentation from freesurfer, ``brainstem``, ``wm`` (white matter), ``thalamicNuclei``, ``hippocampusAmygdala``, ``raphe``, and ``limbic``.
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The ``gtm`` segmentation is a whole-brain segmentation that includes the
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cerebral cortex, subcortical structures, and cerebellum.
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To run the segmentation with the default ``gtm`` method, use: ::
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$ petprep /data/bids_root /out participant --seg gtm
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To run the segmentation with the ``brainstem`` method, use: ::
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$ petprep /data/bids_root /out participant --seg brainstem
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Partial volume correction
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-------------------------
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*PETPrep* can optionally correct PET images for partial volume effects.

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