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[ENH] Add warning about mounting relative paths #690

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9 changes: 7 additions & 2 deletions docs/source/docker.rst
Expand Up @@ -72,11 +72,16 @@ Running mriqc
automatically be executed without need of running the command in item 3.


.. warning::

Paths `<bids_dir>` and `<output_dir>` must be absolute. In particular, specifying relative paths for
`<output_dir>` will generate no error and mriqc will run to completion without error but produce no output.

.. warning::

For security reasons, we recommend to run the docker command with the options
``--read-only --tmpfs /run --tmpfs /tmp``. This will run the docker image in
read-only mode, and map the temporal folders ``/run`` and ``/tmp`` to the temporal
read-only mode, and map the temporary folders ``/run`` and ``/tmp`` to the temporal
folder of the host.


Expand All @@ -87,7 +92,7 @@ Explaining the mriqc-docker command line
Let's dissect this command line:


+ :code:`docker run`- instructs the docker engine to get and run certain
+ :code:`docker run`- instructs the docker engine to get and run a certain
image (which is the last of docker-related arguments:
:code:`poldracklab/mriqc:latest`)
+ :code:`-v <bids_dir>:/data:ro` - instructs docker to mount the local
Expand Down