From 8cafc7ed9afacbb02b6ad66a2b75c810943fb45d Mon Sep 17 00:00:00 2001
From: Pierre <65797646+pierre-nedelec@users.noreply.github.com>
Date: Mon, 23 Dec 2024 14:59:02 -0800
Subject: [PATCH] Add note for nodes without internet access for templateflow

---
 docs/installation.rst | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/installation.rst b/docs/installation.rst
index 8aa21ddf..422359ff 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -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).
+
 
 *********************
 External Dependencies