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DOC: better outline CIFTI / HCP, missed fsLR purge
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docs/outputs.rst

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@@ -143,15 +143,14 @@ mid-thickness surface mesh::
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Surface output spaces include ``fsnative`` (full density subject-specific mesh),
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``fsaverage`` and the down-sampled meshes ``fsaverage6`` (41k vertices) and
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``fsaverage5`` (10k vertices, default). Additionally, the BOLD can be resampled to
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``fsLR`` surfaces, a hybrid version of the ``fsaverage`` atlas with both hemispheres
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in precise geographic correspondence, with varying mesh densities: 32k (default), 59k, and 164k.
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``fsaverage5`` (10k vertices, default).
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**Grayordinates files**.
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CIFTI is a container format that holds both volumetric (regularly sampled in a grid)
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and surface (sampled on a triangular mesh) samples.
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Sub-cortical time series are volumetric (space: ``MNI152NLin6Asym``), while cortical
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time series are sampled to surface (space: ``fsLR``).
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`CIFTI <https://www.nitrc.org/forum/attachment.php?attachid=333&group_id=454&forum_id=1955>`_ is
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a container format that holds both volumetric (regularly sampled in a grid) and surface
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(sampled on a triangular mesh) samples.
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Sub-cortical time series are sampled on a regular grid derived from one MNI template, while
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cortical time series are sampled on surfaces projected from the [Glasser2016]_ template.
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If CIFTI outputs are requested (with the ``--cifti-outputs`` argument), the BOLD series are also
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saved as ``dtseries.nii`` CIFTI2 files::
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@@ -521,6 +520,11 @@ See implementation on :mod:`~fmriprep.workflows.bold.confounds.init_bold_confs_w
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Movement‐Related effects in fMRI time‐series. Magnetic Resonance in Medicine. 1996.
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doi:`10.1002/mrm.191035031 <https://doi.org/10.1002/mrm.1910350312>`_
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.. [Glasser2016] Glasser MF, Coalson TS Robinson EC, Hacker CD, Harwell J, Yacoub E, Ugurbil K,
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Andersson J, Beckmann CF, Jenkinson M, Smith SM, Van Essen DC.
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A multi-modal parcellation of human cerebral cortex. Nature. 2016.
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doi:`10.1038/nature18933 <https://doi.org/10.1038/nature18933>`_
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.. [Hallquist2013] Hallquist MN, Hwang K, Luna B. The Nuisance of Nuisance Regression.
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NeuroImage. 2013. doi:`10.1016/j.neuroimage.2013.05.116
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<https://doi.org/10.1016/j.neuroimage.2013.05.116>`_

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