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DOC: Better describe utilization of custom templates
And close nipreps/smriprep#87 and close #1640 because they will not be implemented anytime soon.
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docs/spaces.rst

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@@ -69,21 +69,29 @@ selecting ``fsLR`` surface space without a density label, ``fsLR:den-32k`` will
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Custom standard spaces
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""""""""""""""""""""""
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Although the functionality is not available yet, the interface of the
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``--output-spaces`` permits providing paths to custom templates that
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follow TemplateFlow's naming conventions
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(e.g., ``/path/to/custom/templates/tpl-MyCustom:res-2``).
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Following the example, at least the following files
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must be found under under ``/path/to/custom/templates/tpl-MyCustom``::
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tpl-MyCustom/
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template_description.json
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tpl-MyCustom_res-1_T1w.nii.gz
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tpl-MyCustom_res-1_desc-brain_mask.nii.gz
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tpl-MyCustom_res-2_T1w.nii.gz
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tpl-MyCustom_res-2_desc-brain_mask.nii.gz
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Although a more comprehensive coverage of standard files would be advised.
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To make your custom templates visible by *fMRIPrep*, and usable via
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the ``--output-spaces`` argument, please store your template under
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*TemplateFlow*'s home directory.
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The default *TemplateFlow*'s home directory is ``$HOME/.cache/templateflow``
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and that can path can be arbitrarily changed by setting
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the ``$TEMPLATEFLOW_HOME`` environment variable.
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A minimal example of the necessary files for a template called
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``MyCustom`` (and therefore callable via, e.g., ``--output-spaces MyCustom``)
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follows::
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$TEMPLATEFLOW_HOME/
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tpl-MyCustom/
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template_description.json
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tpl-MyCustom_res-1_T1w.nii.gz
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tpl-MyCustom_res-1_desc-brain_mask.nii.gz
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tpl-MyCustom_res-2_T1w.nii.gz
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tpl-MyCustom_res-2_desc-brain_mask.nii.gz
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For further information about how custom templates must be organized and
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corresponding naming, please check `the TemplateFlow tutorials
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<https://www.templateflow.org/python-client/tutorials.html>`__.
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For more general information about *TemplateFlow*, visit
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`TemplateFlow.org <https://www.templateflow.org>`__.
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Nonstandard spaces
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""""""""""""""""""

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