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FIX: update documentation
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docs/usage.rst

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@@ -273,7 +273,7 @@ The presets are defined in ``petprep/data/reference_mask/config.json``.
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When a reference mask is created, *PETPrep* also generates a TSV table
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``ref-<name>_morph.tsv`` saved under the ``anat/`` derivatives folder. This
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``label-<name>_desc-ref_morph.tsv`` saved under the ``anat/`` derivatives folder. This
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table mirrors the segmentation morph tables and contains three columns:
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``index``, ``name`` and ``volume-mm3``.
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$ petprep /data/bids_root /out participant \
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--seg gtm --ref-mask-name thalamus --ref-mask-index 10 49
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The indices of the regions from a given segmentation can be found in the corresponding ``/anat/sub-<participant_label>_desc-<segmentation>_morph.tsv``.
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The indices of the regions from a given segmentation can be found in the corresponding ``/anat/sub-<participant_label>_seg-<segmentation>_morph.tsv``.
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Troubleshooting
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---------------

docs/workflows.rst

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@@ -560,7 +560,7 @@ image ``seg-<seg>_dseg.nii.gz`` and a TSV table of region volumes
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``seg-<seg>_morph.tsv`` saved under the ``anat/`` derivatives folder.
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Reference masks generated via ``--ref-mask-name`` create a similar
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``ref-<name>_morph.tsv`` file. These TSVs share the same columns as the
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``label-<name>_desc-ref_morph.tsv`` file. These TSVs share the same columns as the
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segmentation morph tables: ``index``, ``name`` and ``volume-mm3``.
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For example, the raphe segmentation can be enabled with::

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