Add quick CIVET tutorial

FNNDSC · Nov 13, 2024 · a774a81 · a774a81
1 parent 13aa8ff
commit a774a81
Show file tree

Hide file tree

Showing 6 changed files with 56 additions and 0 deletions.
diff --git a/docs/tutorials/civet/add_pipeline.png b/docs/tutorials/civet/add_pipeline.png
diff --git a/docs/tutorials/civet/index.md b/docs/tutorials/civet/index.md
@@ -0,0 +1,56 @@
+---
+title: Running CIVET on ChRIS at FNNDSC
+---
+
+# Running CIVET on _ChRIS_ at FNNDSC
+
+_CIVET_ is a T1 MRI processing pipeline (similar to FreeSurfer) developed at the Montréal Neurological Institute (MNI). This tutorial is a beginner-level walk-through of how to run _CIVET_ on _ChRIS_ at the FNNDSC.
+
+### 1. Log in to _ChRIS_
+
+Go to **http://chris-next.tch.harvard.edu:2222/login** and log in using your FNNDSC account username and password.
+
+### 2. Create a feed
+
+Data are uploaded into _ChRIS_ in _feeds._
+
+1. Click **"Create Feed"** in the top-right corner. 
+2. Choose the **"Generate Data"** option.
+3. Select the `pl-neurofiles-pull` plugin, which pulls data from `/neuro/labs/grantlab/research` into _ChRIS_.
+4. Specify which path to pull as the `--path` parameter.
+5. Keep clicking "Next" until the feed is created.
+
+![Screenshot of creating a feed in _ChRIS_](./select_data.png)
+
+The path you choose _must_ be a directory containing exactly one _NIFTI_ file called `*_T1w.nii`.
+Any unrelated files (such as `*.json`, `*._T2w.nii`) will also be uploaded to _ChRIS_ but ignored by the pipeline.
+
+### 3. Run the pipeline
+
+Click into the feed you just created, and right-click the only circle in the top-left quadrant. Select **"Add a pipeline."**
+
+![Screenshot of feed view](./add_pipeline.png)
+
+Search for the "CIVET" pipeline and select it.
+
+::::danger
+
+Carefully review the pipeline's options before you run it. Make sure that each step of the pipeline is configured to run on **"galena,"** our private compute cluster. You may also choose "NERC," a public cloud, as long as your data does not contain PHI.
+
+::::
+
+![Screenshot of pipeline configuration](./select_pipeline.png)
+
+Once the pipeline is running, you can see each of its steps and their statuses. You can see that the pipeline selects the `*_T1w.nii` file, renames it to `*_t1.nii`, then converts it to MINC.
+
+![Screenshot of the pipeline as its running](./running.png)
+
+### 4. Wait a couple hours
+
+CIVET takes 4-8 hours to run to completion.
+
+## Next Steps
+
+You now know how to run _CIVET_ using the _ChRIS_ user interface.
+Next steps might include visualization and downstream analyses of _CIVET_
+outputs, or scaling up to run this pipeline on multiple subjects.
diff --git a/docs/tutorials/civet/parameters.png b/docs/tutorials/civet/parameters.png
diff --git a/docs/tutorials/civet/running.png b/docs/tutorials/civet/running.png
diff --git a/docs/tutorials/civet/select_data.png b/docs/tutorials/civet/select_data.png
diff --git a/docs/tutorials/civet/select_pipeline.png b/docs/tutorials/civet/select_pipeline.png