Improve documentation for running QSIPrep with TemplateFlow on non-in…

…ternet nodes (#907)

* Add note for nodes without internet access for templateflow

* Clean update to docs regarding non-internet node usage for rst

* Update docs/installation.rst

---------

Co-authored-by: Matt Cieslak <mattcieslak@gmail.com>

docs/installation.rst

@@ -97,6 +97,39 @@ 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 with Apptainer 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, when running with ``--containall``, the default location may not be accessible, and any 
+    missing templates will be tentatively downloaded into the temporary QSIPrep working directory instead.
+    To avoid this, you must always set and bind ``TEMPLATEFLOW_HOME`` explicitly.
+
+    Steps to ensure successful execution:
+
+    1. On an **internet-enabled node**, set and bind the ``TEMPLATEFLOW_HOME`` variable to a persistent 
+       directory before running QSIPrep. This will ensure all necessary templates are downloaded into the 
+       specified location:
+
+       .. code-block:: sh
+    
+          export TEMPLATEFLOW_HOME=/path/to/persistent/templateflow
+          apptainer run --cleanenv --containall \
+            -B ${TEMPLATEFLOW_HOME}:${TEMPLATEFLOW_HOME} \
+            --env "TEMPLATEFLOW_HOME=$TEMPLATEFLOW_HOME" \
+            /path/to/qsiprep_<VERSION>.sif <your commands>
+
+    2. If the ``TEMPLATEFLOW_HOME`` directory is not accessible on your target HPC node, manually copy it 
+       to the target system after the first run.
+
+    3. On nodes without internet access, bind the copied ``TEMPLATEFLOW_HOME`` directory and set the 
+       environment variable as described above before running QSIPrep.
+     4. It may help to run a single subject or session on its own before running many jobs that access the templates. The single run will download the necessary templates and prevent multiple jobs from attempting to download the templates simultaneously.
+
+
+    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