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Improve documentation for running QSIPrep with TemplateFlow on non-internet nodes #907

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merged 3 commits into from
Feb 3, 2025

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pierre-nedelec
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Changes proposed in this pull request

This pull request improves the QSIPrep documentation by adding detailed guidance for configuring TEMPLATEFLOW_HOME when running QSIPrep on nodes without internet access. Specifically:

  • Clarifies the behavior of QSIPrep when using --containall, emphasizing the need to explicitly set and bind TEMPLATEFLOW_HOME.
  • Provides step-by-step instructions for ensuring required templates are pre-fetched and made available in offline environments.
  • Includes usage examples for both internet-enabled and non-internet nodes to streamline the workflow.
  • Links to relevant resources, including the fMRIPrep FAQ and a Neurostars thread discussing similar issues.

These changes address user confusion regarding offline usage of QSIPrep with TemplateFlow and improve the documentation for both first-time and advanced users.

Documentation that should be reviewed

The primary changes are located in the section detailing Apptainer usage docs/installation.rst.

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codecov-commenter commented Dec 24, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 45.80%. Comparing base (fa4dbe0) to head (b76b0ce).
Report is 2 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #907      +/-   ##
==========================================
+ Coverage   44.23%   45.80%   +1.57%     
==========================================
  Files          66       65       -1     
  Lines        9839     9722     -117     
  Branches     1097     1063      -34     
==========================================
+ Hits         4352     4453     +101     
+ Misses       5263     5041     -222     
- Partials      224      228       +4     

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@tsalo tsalo requested a review from mattcieslak January 13, 2025 13:16
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@mattcieslak mattcieslak left a comment

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Thank you @pierre-nedelec! I added one suggestion

@tsalo tsalo changed the title [DOC] Improve Documentation for Running QSIPrep with TemplateFlow on Non-Internet Nodes Improve documentation for running QSIPrep with TemplateFlow on non-internet nodes Feb 3, 2025
@tsalo tsalo merged commit 46579b3 into PennLINC:master Feb 3, 2025
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4 participants