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enh: complete suggestions from @yarikoptic
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Related-to: nipreps/nipreps.github.io#47 (comment)
Co-authored-by: Yaroslav Halchenko <[email protected]>
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oesteban and yarikoptic committed Jan 6, 2025
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Expand Up @@ -19,7 +19,7 @@ tip and troubleshooting guidelines for both
`Singularity or Apptainer <https://www.nipreps.org/apps/singularity/>`__.
In addition to container-specific guidelines, the documentation
also includes specific
`help for processing DataLad-managed datasets <https://www.nipreps.org/apps/datalad/>`__
`help for processing DataLad-managed datasets <https://www.nipreps.org/apps/datalad/>`__.

The rest of this documentation page applies to both *bare-metal*
and containerized execution modes.
Expand Down Expand Up @@ -86,6 +86,21 @@ in :ref:`The MRIQC Reports <reports>`.
In the ``group`` level, the :abbr:`IQMs (image quality metrics)` extracted in
first place are combined in a table and the group reports are generated.

*MRIQC* can fetch data in *DataLad* datasets
--------------------------------------------
As of *MRIQC* 22.0.3, the application bundles *DataLad*, enabling automatic
data fetching in *DataLad* datasets.
Employing this feature in containerized environments may lead to
somewhat obscure errors (see, for example,
`nipreps/mriqc#1307 <https://github.com/nipreps/mriqc/issues/1307>`__.
If you intend to use *DataLad* datasets, please read carefully
*NiPreps*' `help for processing DataLad-managed datasets <https://www.nipreps.org/apps/datalad/>`__.

Alternatively, this feature can be disabled by adding
``--no-datalad-get`` to the command line.
This will separate *DataLad* management from *MRIQC*'s operation,
which can be an effective way of debugging and averting these issues.

Command line interface
----------------------
.. argparse::
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