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Add note for nodes without internet access for templateflow
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pierre-nedelec authored Dec 23, 2024
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Expand Up @@ -97,6 +97,29 @@ As with Docker, you will need to bind the Freesurfer license.txt when running Ap
$HOME/fullds005 $HOME/dockerout participant \
--fs-license-file /opt/freesurfer/license.txt

.. note::
**Running QSIPrep on Non-Internet Nodes:**
QSIPrep relies on TemplateFlow to provide standard anatomical templates. By default, it downloads
necessary files into the ``$TEMPLATEFLOW_HOME`` directory (default: ``$HOME/.cache/templateflow``).
However, on nodes without internet access, this will cause job failure unless the required templates
are pre-fetched and available.

1. Run QSIPrep once on an internet-enabled node. This will automatically download the required
templates into the ``$TEMPLATEFLOW_HOME`` directory (or ``$HOME/.cache/templateflow`` if the variable
is unset).
2. If the directory is not accessible on the target HPC node, copy it manually to the target system.
3. Bind and pass the ``TEMPLATEFLOW_HOME`` variable to the container:
```sh
export TEMPLATEFLOW_HOME=/path/to/copied/templateflow
apptainer run --cleanenv --containall \
-B ${TEMPLATEFLOW_HOME}:${TEMPLATEFLOW_HOME} \
--env "TEMPLATEFLOW_HOME=$TEMPLATEFLOW_HOME" \
/path/to/qsiprep_<VERSION>.sif <your commands>
```

For additional troubleshooting, see [fmriprep docs](https://fmriprep.org/en/stable/faq.html#how-do-you-use-templateflow-in-the-absence-of-access-to-the-internet)
or [this thread on Neurostars](https://neurostars.org/t/issue-with-qsiprep-templateflow-on-hpc-host-with-no-internet-access/31259/10?u=pierre-nedelec).


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External Dependencies
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