neuropoly · RignonNoel · Jul 26, 2022 · Jul 26, 2022 · Jul 26, 2022 · Jul 26, 2022
diff --git a/bibliography/mri.md b/bibliography/mri.md
@@ -30,7 +30,7 @@
 
 * [Jupyter book](https://shimming-toolbox.github.io/B1-shimming/) covering the basics of static B1+ shimming
 * [Gaspard Cereza's MSc thesis](https://www.dropbox.com/s/4cv8s4t0ioll32q/Master_thesis_Gaspard_Cereza_corrected_2.pdf?dl=0)
-* [🔒 🎥 Universal Pulse]() TODO
+* 🔒 🎥 Universal Pulse TODO
 * [🔒 VOP creation (internal documentation)](https://docs.google.com/document/d/1uqr4UX4VY8H8cZ_DB9zaj12o0xrswRj44AxE3FZauHM/edit#heading=h.uf4xboevl4xa)
 @Gaspard todo: (notably list talks from UHF meeting)
 

diff --git a/computing-resources/data/duke.md b/computing-resources/data/duke.md
@@ -20,7 +20,7 @@ The shared folders are:
 
 ## Access from stations
 
-When [connecting with `ssh`](../../#ssh-command-line), `duke` is available at `/mnt/duke/`, e.g.:
+When [connecting with `ssh`](../neuropoly/README.md#ssh-command-line), `duke` is available at `/mnt/duke/`, e.g.:
 
 ```
 u932945@joplin:~$ ls -l /mnt/duke
@@ -36,7 +36,7 @@ drwxr-xr-x 2 u108545 domain users  4096 Jun  8 16:44 temp
 
 ## Mount with GUI
 
-When working on campus or [over the VPN](../../#vpn), you can connect your computer to `duke`:
+When working on campus or [over the VPN](../neuropoly/README.md#vpn), you can connect your computer to `duke`:
 
 ````{tabbed} macOS
 1. Open Finder

diff --git a/computing-resources/data/git-datasets.md b/computing-resources/data/git-datasets.md
@@ -4,16 +4,16 @@ This server includes private MRI and microscopy datasets, which have been curate
 
 `git+ssh://data.neuro.polymtl.ca` has a max size of ~1TB.
 
-It hosts [BIDS](https://bids-specification.readthedocs.io) datasets, version-controlled using [`git-annex`](git-annex.branchable.com/).
-It is locked behind a [VPN](../../#vpn) because much of our data is under medical ethics protections, and needs to be kept off the general internet.
+It hosts [BIDS](https://bids-specification.readthedocs.io) datasets, version-controlled using [`git-annex`](https://git-annex.branchable.com/).
+It is locked behind a [VPN](../neuropoly/README.md#vpn) because much of our data is under medical ethics protections, and needs to be kept off the general internet.
 
 
 Initial setup
 -------------
 
 ### Prerequisites
 
-0. You must have a \*nix OS with `git-annex>=8` installed. See [`git-annex` installation](./git-annex.md#installation).
+0. You must have a \*nix OS with `git-annex>=8` installed. See [`git-annex` installation](../../geek-tips/git-annex.md#installation).
 2. Make sure you have an ssh key.
     * If not, run `ssh-keygen -t ed25519 -C [email protected]`. Your keys will be in the hidden folder `~/.ssh/`.
 
@@ -50,7 +50,7 @@ Because this server contains private medical data, you need to be on campus, con
 
 *If connecting from off-campus*, connect to [polyvpn](http://www.polymtl.ca/si/reseaux/acces-securise-rvp-ou-vpn).
 
-> 🏚️ Verify connectivity by `ping data.neuro.polymtl.ca`. If **you cannot ping** then you need to double-check your VPN connection; make sure it is connected, make sure you can reach `joplin`, and if it still isn't working *ask the [Poly network admins]([email protected])* to unblock your account from this server.
+> 🏚️ Verify connectivity by `ping data.neuro.polymtl.ca`. If **you cannot ping** then you need to double-check your VPN connection; make sure it is connected, make sure you can reach `joplin`, and if it still isn't working *ask the [Poly network admins](mailto:[email protected])* to unblock your account from this server.
 
 Verify you can use the server by `ssh [email protected] help`. If it hangs, triple-check again your VPN. If it rejects you, your account is not created yet, or you have switched machines. A successful connection looks like:
 
@@ -78,7 +78,7 @@ Usage
 
 During daily usage, you will need to be [*on the polyvpn network*](#connection).
 
-You should also make sure to [configure git annex](./git-annex.md#global-git-config) for the best performance.
+You should also make sure to [configure git annex](../../geek-tips/git-annex.md#global-git-config) for the best performance.
 
 ### List
 
@@ -159,7 +159,7 @@ git annex sync --no-content --only-annex
 git push
 ```
 
-Finally, ask one of that dataset's reviewers to [look at your pull request](#Reviewing-Pull-Requests) by opening an issue on [neuropoly/data-management](https://github.com/neuropoly/data-management).
+Finally, ask one of that dataset's reviewers to [look at your pull request](#reviewing-pull-requests) by opening an issue on [neuropoly/data-management](https://github.com/neuropoly/data-management).
 
 
 ### Reviewing Pull Requests
@@ -232,7 +232,7 @@ git push origin :synced/xy/branchname
 
 ### New repository
 
-To make a new repo, follow this [recipe](./git-annex.md#new-repo).
+To make a new repo, follow this [recipe](../../geek-tips/git-annex.md#new-repo).
 
 Then, to upload it, pick a name under `datasets/`, e.g. "my-new-repo", and do
 

diff --git a/computing-resources/neuropoly/README.md b/computing-resources/neuropoly/README.md
@@ -25,7 +25,7 @@ getent passwd <GRAMES_ACCOUNT>
 
 ### Home folder
 
-Every [GRAMES](../#poly-grames) account has a school-wide personal home folder. It is backed-up nightly.
+Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.
 
 ````{tabbed} macOS
 1. Open Finder
@@ -252,7 +252,7 @@ will attach the remote `/tmp/` to the local `./cluster_folder`
 
 
 ```{note}
-If you are experiencing mounting issues on macOs, [this]([url](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57)) might help.
+If you are experiencing mounting issues on macOs, [this](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57) might help.
 ```
 
 

diff --git a/computing-resources/neuropoly/cpus.md b/computing-resources/neuropoly/cpus.md
@@ -4,7 +4,7 @@ description: How to use CPU clusters at Neuropoly
 
 # CPU Clusters
 
-Unless otherwise stated, use your [connect with your polygrames credentials](./computing-resources-neuropoly.md#TODO)
+Unless otherwise stated, use your [connect with your polygrames credentials](README.md)
 
 ## `joplin`
 

diff --git a/computing-resources/neuropoly/gpus.md b/computing-resources/neuropoly/gpus.md
@@ -1035,7 +1035,7 @@ You can also see all this information plotted over time for each machine at
 * [https://monitor.neuro.polymtl.ca/host/rosenberg.neuro.polymtl.ca/](https://monitor.neuro.polymtl.ca/host/rosenberg.neuro.polymtl.ca/)
 * [https://monitor.neuro.polymtl.ca/host/romane.neuro.polymtl.ca/](https://monitor.neuro.polymtl.ca/host/romane.neuro.polymtl.ca/)
 
-#### Monitoring GPUs
+### Monitoring GPUs
 
 As above, you can see the computation amount, allocated RAM, temperature, fan speed of the GPUs on the command line with
 

diff --git a/computing-resources/printer.md b/computing-resources/printer.md
@@ -7,7 +7,7 @@ IP address: See [NeuroPoly Internal Document: Printer](https://docs.google.com/d
 
 ## Troubleshooting
 
-#### Brother HL-3170CDW - Error: "low toner" <a id="misc_-_brother_hl-3170cdw_-_errorlow_toner"></a>
+### Brother HL-3170CDW - Error: "low toner" <a id="misc_-_brother_hl-3170cdw_-_errorlow_toner"></a>
 
 If it doesn't print and it says “low toner” on the printer, do the following:
 

diff --git a/conf.py b/conf.py
@@ -52,7 +52,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_book_theme'
+html_theme = 'furo'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -68,15 +68,9 @@
 html_sourcelink_suffix = ".md" # our sources are in markdown; but this only has an effect if "use_download_button": True
 
 html_theme_options = {
-    "toc_title": "Page Contents",
-    "search_bar_text": "Search...",
-
-    "repository_url": "https://github.com/neuropoly/intranet.neuro.polymtl.ca",
-    "use_fullscreen_button": False,
-    "use_edit_page_button": True,
-    "use_download_button": False,
-
-    #"logo_only": True, # hides html_title and just shows html_logo
+    "sidebar_hide_name": False,
+    "source_repository": "https://github.com/neuropoly/intranet.neuro.polymtl.ca",
+    "source_branch": "master",
 }
 
 

diff --git a/geek-tips/contributing.md b/geek-tips/contributing.md
@@ -7,7 +7,7 @@ First off, thanks for taking the time to contribute to one of **NeuroPoly**'s pr
 This set of guidelines provides general instruction on how to make any one of the following contributions:
 
 * Submitting a bug report or feature request (See: [Opening an Issue](#opening-an-issue-on-github))
-* Fixing a bug or developing a feature (See: [Developing](#developing) and [Submitting a Pull Request](#submitting-a-pull-request))
+* Fixing a bug or developing a feature (See: [Developing](#developing-code) and [Submitting a Pull Request](#submitting-a-pull-request))
 
 ## Project-Specific Guidance
 

diff --git a/geek-tips/deep-learning/README.md b/geek-tips/deep-learning/README.md
@@ -19,7 +19,7 @@ misc
 
 
 
-### Frameworks/Libraries <a id="frameworkslibraries"></a>
+## Frameworks/Libraries <a id="frameworkslibraries"></a>
 
 [https://github.com/kjw0612/awesome-deep-vision](https://github.com/kjw0612/awesome-deep-vision)
 

diff --git a/geek-tips/deep-learning/tensorflow.md b/geek-tips/deep-learning/tensorflow.md
@@ -12,7 +12,7 @@ export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY
 export CUDA_HOME=/usr/local/cuda
 ```
 
-### Install tensorflow <a id="install_tensorflow"></a>
+## Install tensorflow <a id="install_tensorflow"></a>
 
 ```bash
 # This is for install tensorflow with GTX1080 drvier.
@@ -72,22 +72,22 @@ python test_tensorflow.py
 echo ------------------- End script -------------------
 ```
 
-### Fix CUDA driver version <a id="fix_cuda_driver_version"></a>
+## Fix CUDA driver version <a id="fix_cuda_driver_version"></a>
 
 ```bash
 sudo add-apt-repository ppa:graphics-drivers/ppa
 sudo apt-get update
 sudo apt-get install nvidia-367
 ```
 
-### Fix module tensorflow import error <a id="fix_module_tensorflow_import_error"></a>
+## Fix module tensorflow import error <a id="fix_module_tensorflow_import_error"></a>
 
 ```bash
 sudo pip uninstall six
 sudo pip install six --upgrade --target="/usr/lib/python2.7/dist-packages"
 ```
 
-### Reference <a id="reference"></a>
+## Reference <a id="reference"></a>
 
 [Install with GPU support](https://github.com/uher/InstallGpuEnableTensorflow)
 
diff --git a/geek-tips/git-annex.md b/geek-tips/git-annex.md
@@ -1,6 +1,6 @@
 # git-annex
 
-[`git annex`](git-annex.branchable.com/) is an extension to git that lets it handle large repos spread in pieces across multiple servers/disks/accounts.
+[`git annex`](https://git-annex.branchable.com/) is an extension to git that lets it handle large repos spread in pieces across multiple servers/disks/accounts.
 
 We are using it because
 
@@ -73,7 +73,7 @@ git config --global annex.thin true # save disk space by de-duplicating checked
 git config --global annex.private true # prevent attempting to share your local copy of the annex, which is impossible when working in a team
 ```
 
-See [below](#hardlinks) to understand what this setting offers.
+See [below](#annexthin-hardlinks) to understand what this setting offers.
 
 ## New repo
 

diff --git a/geek-tips/image-processing-software/diffusion-simulator.md b/geek-tips/image-processing-software/diffusion-simulator.md
@@ -14,7 +14,7 @@ You can choose the permeability of the barriers via p but not the thickness.
 
 However, you can also build any kind of shape using a PLY file \(3D object file\). Here is a tutorial for this option: [Monte-Carlo Mesh Simulation](http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCMeshSimulation).
 
-### Recommendations <a id="advices"></a>
+## Recommendations <a id="advices"></a>
 
 * `cylindersep` must be at least twice as big as `cylinderrad` \(cylinders mustn't overlap\)
 * Be very careful at high q-values \(&gt;0.14 um-1\). You need lots of walkers \(200 000\), and time steps \(-tmax 3000\)

diff --git a/geek-tips/image-processing-software/itk-snap.md b/geek-tips/image-processing-software/itk-snap.md
@@ -2,7 +2,7 @@
 
 [ITK-SNAP](http://www.itksnap.org/pmwiki/pmwiki.php) is a software package used to segment structures in 3D medical images.
 
-### Create a mesh out of a binary file <a id="create_a_mesh_out_of_a_binary_file"></a>
+## Create a mesh out of a binary file <a id="create_a_mesh_out_of_a_binary_file"></a>
 
 ITK-SNAP allows you to construct a mesh \(`.vtk`\) with a binary mask.
 

diff --git a/geek-tips/misc/docker/README.md b/geek-tips/misc/docker/README.md
@@ -17,29 +17,29 @@ docker-for-deep-learning
 
 ## Using Docker
 
-#### Search for remote image
+### Search for remote image
 
 ```text
 docker search ubuntu  # will search for ubuntu distrib
 ```
 
 [List of Ubuntu images](https://hub.docker.com/_/ubuntu)
 
-#### Install & Run Linux distribution <a id="install_run_linux_distribution"></a>
+### Install & Run Linux distribution <a id="install_run_linux_distribution"></a>
 
 ```text
 docker pull debian  # will install debian
 docker pull ubuntu:16.04
 docker pull centos
 ```
 
-#### List local Docker images <a id="list_local_docker_images"></a>
+### List local Docker images <a id="list_local_docker_images"></a>
 
 ```text
 docker images
 ```
 
-#### Run Docker image <a id="run_docker_image"></a>
+### Run Docker image <a id="run_docker_image"></a>
 
 To run in interactive mode, use flag `-i`
 
@@ -49,15 +49,15 @@ docker run -it ubuntu:trusty /bin/bash
 docker run -it ubuntu:16.04
 ```
 
-#### Remove Docker image or containers \(force deletion\) <a id="remove_docker_image_or_containers_force_deletion"></a>
+### Remove Docker image or containers \(force deletion\) <a id="remove_docker_image_or_containers_force_deletion"></a>
 
 ```text
 docker rmi -f IMAGE_ID
 docker rmi $(docker images -a -q)  # WARNING!!! This will remove all images
 docker rm $(docker ps -a -f status=exited -q)  # WARNING!!! This will remove all containers
 ```
 
-#### Save a Docker image <a id="save_a_docker_image"></a>
+### Save a Docker image <a id="save_a_docker_image"></a>
 
 The example below shows how to install useful items on a standard ubuntu image, and then save the image locally.
 
@@ -75,7 +75,7 @@ docker ps -a
 docker commit <container_id> your_name/ubuntu:16.04
 ```
 
-#### Build Docker container from Dockerfile <a id="build_docker_container_from_dockerfile"></a>
+### Build Docker container from Dockerfile <a id="build_docker_container_from_dockerfile"></a>
 
 1. Create a Dockerfile by running \`touch Dockerfile\`
 2. Inside the Dockerfile write the following \(items below are just given as an example\):
@@ -105,7 +105,7 @@ ENV PATH "/sct/bin:${PATH}"
 1. Build docker image: \`docker build -t &lt;container\_id&gt; .\`
 2. Run it: \`docker run -it &lt;container\_id&gt;\`
 
-#### Run with DISPLAY redirection <a id="run_with_display_redirection"></a>
+### Run with DISPLAY redirection <a id="run_with_display_redirection"></a>
 
 In order to run scripts with GUI you need to allow X11 redirection:
 
@@ -117,7 +117,7 @@ In order to run scripts with GUI you need to allow X11 redirection:
    1. On OSX: \`docker run -e DISPLAY=host.docker.internal:0 -it &lt;CONTAINER\_ID&gt;\`
    2. On Linux: \`docker run -ti –rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix &lt;CONTAINER\_ID&gt;\`
 
-#### Copy file into container <a id="copy_file_into_container"></a>
+### Copy file into container <a id="copy_file_into_container"></a>
 
 ```bash
 # list container
Original file line number	Diff line number	Diff line change
Expand Up		@@ -19,7 +19,7 @@ misc



		### Frameworks/Libraries <a id="frameworkslibraries"></a>
		## Frameworks/Libraries <a id="frameworkslibraries"></a>

		[https://github.com/kjw0612/awesome-deep-vision](https://github.com/kjw0612/awesome-deep-vision)

Expand Down