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Co-authored-by: Taylor Salo <[email protected]>
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docs/workflows.rst

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@@ -178,18 +178,18 @@ In the case of multiple T1w images (across sessions and/or runs), *fMRIPrep* pro
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a few choices on how to generate the reference anatomical space.
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If ``--subject-anatomical-reference first-lex`` is used, all T1w images are
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merged into a single template image using FreeSurfer's `mri_robust_template`_, aligned
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merged into a single template image using FreeSurfer's `mri_robust_template`_,
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aligned to the first image (determined lexicographically by session label). This is
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the default behavior.
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If ``--subject-anatomical-reference unbiased`` is used, all T1w images are merged into
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a an *unbiased* template, or equidistant from all source images.
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an *unbiased* template, equidistant from all source images.
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For two images, the additional cost of estimating an unbiased template is trivial,
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but aligning three or more images is too expensive to justify being the default behavior.
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If ``--subject-anatomical-reference sessionwise`` is used, a reference template will be
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generated for each session independently. If multiple T1w images are found within a session,
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other images will align to the first lexicographical image.
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the images will be aligned to the first lexicographical image from that session.
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.. note::
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