diff --git a/books/_config.yml b/books/_config.yml index 21b62b92..6e765e6b 100644 --- a/books/_config.yml +++ b/books/_config.yml @@ -11,7 +11,7 @@ only_build_toc_files: true # See https://jupyterbook.org/content/execute.html execute: execute_notebooks: force - allow_errors: true + allow_errors: false timeout: 45000 stderr_output: show run_in_temp: true @@ -37,13 +37,21 @@ html: use_repository_button: true use_download_button: true use_edit_page_button: true - google_analytics_id: G-4Z9774J59Y + analytics: + google_analytics_id: G-4Z9774J59Y sphinx: config: nb_code_prompt_hide: "outputs" nb_merge_streams: true mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js + html_css_files: ['algolia.css', 'https://cdn.jsdelivr.net/npm/@docsearch/css@3'] + html_js_files: [ + 'https://cdn.jsdelivr.net/npm/@docsearch/js@3.3.3/dist/umd/index.js', + 'algolia.js' + ] + html_static_path: ['_static'] + html_extra_path: ['_static'] parse: myst_enable_extensions: diff --git a/books/_static/docsearch.css b/books/_static/docsearch.css deleted file mode 100644 index d233e14e..00000000 --- a/books/_static/docsearch.css +++ /dev/null @@ -1,8 +0,0 @@ -/** - * Skipped minification because the original files appears to be already minified. - * Original file: /npm/@docsearch/css@3.8.0/dist/style.css - * - * Do NOT use SRI with dynamically generated files! 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-//# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/books/diffusion_imaging/MRtrix_Preprocessing.ipynb b/books/diffusion_imaging/MRtrix_Preprocessing.ipynb index 472a275c..1a6416c7 100644 --- a/books/diffusion_imaging/MRtrix_Preprocessing.ipynb +++ b/books/diffusion_imaging/MRtrix_Preprocessing.ipynb @@ -465,19 +465,6 @@ "To see how this works, navigate to the folder sub-CON02/ses-preop/dwi, which contains the diffusion data. One of the first steps for preprocessing your data is converting the diffusion data to a format that MRtrix understands; we will use the command ```mrconvert``` to combine the raw diffusion data with its corresponding ```.bval``` and ```.bvec files```, so that we can use the combined file for future preprocessing steps:" ] }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "# Save the original directory\n", - "# original_dir = os.getcwd()\n", - "# Navigate to the diffusion data\n", - "# os.chdir(\"ds001226/sub-CON02/ses-preop/dwi\")\n", - "# os.getcwd()" - ] - }, { "cell_type": "code", "execution_count": 7,