Merge pull request #23 from josephmje/gh-pages

MISC: File organization and binder updates
carpentries-incubator · May 27, 2021 · ec87810 · ec87810
2 parents bf7cbe2 + 2b46270
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Showing 15 changed files with 116 additions and 14 deletions.
diff --git a/.github/workflows/notebook.yml b/.github/workflows/notebook.yml
@@ -1,10 +1,11 @@
 name: Test notebooks
 
 on:
-  push
+  push:
+    paths: "*.ipynb"
 
 jobs:
-  build:
+  test-notebooks:
     if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
     strategy:
@@ -26,28 +27,25 @@ jobs:
       uses: actions/cache@v2
       id: cache
       with:
-        path: .cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        path: ${{ env.pythonLocation }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
         restore-keys: |
-          ${{ runner.os }}-pip-
+          ${{ env.pythonLocation }}-
 
     # Install all requirements to run these tests.
     - name: Install requirements
       if: steps.cache.outputs.cache-hit != 'true'
       run: |
         python -m pip install --upgrade pip
-        pip3 install virtualenv
-        virtualenv ~/dc_venv
         pip install -r requirements.txt
         pip install pytest nbval
 
     # Download the necessary data
     - name: Download data
       run: |
-        osf -p cmq8a clone ./data
+        datalad install
 
     # Run the actual tests of all the Python Notebooks.
     - name: Test Notebooks
       run: |
-        source ~/dc_venv/bin/activate
-        pytest --nbval-lax -v code/*/*.ipynb
+        pytest --nbval-lax -v code/*_solutions.ipynb
diff --git a/_config.yml b/_config.yml
@@ -10,7 +10,7 @@
 carpentry: "incubator"
 
 # Overall title for pages.
-title: "Introduction to MRI Data Analysis"
+title: "Introduction to Working with MRI Data in Python"
 
 # Life cycle stage of the lesson
 # possible values: "pre-alpha", "alpha", "beta", "stable"
@@ -70,7 +70,9 @@ collections:
 
 # Manual episode order
 episode_order:
+  - introduction
   - anatomy-of-nifti
+  - data-organization
   - open-mri-datasets
 
 # Set the default layout for things in the episodes collection.

diff --git a/_episodes/data-organization.md b/_episodes/data-organization.md
@@ -0,0 +1,11 @@
+---
+title: "Data Organization with BIDS"
+teaching: 30
+exercises: 15
+questions:
+- ""
+objectives:
+- ""
+keypoints:
+- ""
+---
diff --git a/_episodes/introduction.md b/_episodes/introduction.md
@@ -0,0 +1,47 @@
+---
+title: "Neuroimaging Fundamentals"
+teaching: 20
+exercises: 10
+questions:
+- ""
+objectives:
+- ""
+keypoints:
+- ""
+---
+
+## Why Python?
+
+- free, open source
+- one platform for data pre-processing, visualization and analysis
+- reproducible code
+- large number of user-developed packages (eg. nibabel, nilearn)
+- easy interaction with state-of-the art neuroimaging software (eg. FSL, ANTS)
+
+## Types of MR Scans
+
+![mr-scan-types](../fig/mr_scan_types.png){:class="img-responsive"}
+
+anat
+
+func
+
+dwi
+
+## Neuroimaging File Formats
+
+|Format Name | File Extension | Origin |
+|---|---|---|
+| Analyze | .img/.hdr | Analyze Software, Mayo Clinic |
+| DICOM | none | ACR/NEMA Consortium |
+| NIfTI | .nii or .img/.hdr | Neuroimaging Informatics Technology Initiative |
+| MINC | .mnc | Montreal Neurological Institute |
+| NRRD | .nrrd | |
+
+![dicom-to-nifti](../fig/dicom_to_nifti.png){:class="img-responsive"}
+
+From the MRI scanner, images are initially collected in the DICOM format and can be converted to NIfTI using [dcm2niix](https://github.com/rordenlab/dcm2niix).
+
+## Intro to NIfTI
+
+NIfTI is one of the most ubiquitous file formats for storing neuroimaging data. We'll cover a few details to get started working with them. If you're interested in learning more about NIfTI images, we highly recommend [this blog post about the NIfTI format](http://brainder.org/2012/09/23/the-nifti-file-format/).
diff --git a/_episodes/reproducible-workflows.md b/_episodes/reproducible-workflows.md
@@ -0,0 +1,11 @@
+---
+title: "Reproducible Workflows"
+teaching: 30
+exercises: 15
+questions:
+- ""
+objectives:
+- ""
+keypoints:
+- ""
+---
diff --git a/binder/apt.txt b/binder/apt.txt
@@ -0,0 +1 @@
+tree
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -0,0 +1,21 @@
+name: dataviz_python
+
+channels:
+  - default
+  - conda-forge
+
+dependencies:
+  - python=3.8.*
+  - pip
+  - git
+  - git-annex
+  - datalad=0.14.4
+  - matplotlib
+  - nibabel
+  - numpy
+  - pandas
+  - texinfo
+
+  - pip:
+      - pybids
+      - datalad-installer
diff --git a/binder/postBuild b/binder/postBuild
@@ -0,0 +1,11 @@
+# Git set up
+git config --global --add user.name "Ford Escort"
+git config --global --add user.email [email protected]
+
+# Get data
+
+openneuro_dataset=ds000030
+
+datalad clone "https://github.com/OpenNeuroDatasets/${openneuro_dataset}.git" "data/${openneuro_dataset}/"
+datalad get data/${openneuro_dataset}/sub-01/anat/*
+datalad get data/${openneuro_dataset}/sub-01/func/sub-01_task-compL1_run-1_bold.*
diff --git a/...entals/01-neuroimaging-fundamentals.ipynb → code/01-neuroimaging-fundamentals.ipynb b/...entals/01-neuroimaging-fundamentals.ipynb → code/01-neuroimaging-fundamentals.ipynb
diff --git a/...natomy-of-nifti/02-anatomy-of-nifti.ipynb → code/02-anatomy-of-nifti.ipynb b/...natomy-of-nifti/02-anatomy-of-nifti.ipynb → code/02-anatomy-of-nifti.ipynb
diff --git a/...tions/02-anatomy-of-nifti_solutions.ipynb → code/02-anatomy-of-nifti_solutions.ipynb b/...tions/02-anatomy-of-nifti_solutions.ipynb → code/02-anatomy-of-nifti_solutions.ipynb
diff --git a/...ure/03-brain-imaging-data-structure.ipynb → code/03-brain-imaging-data-structure.ipynb b/...ure/03-brain-imaging-data-structure.ipynb → code/03-brain-imaging-data-structure.ipynb
diff --git a/...n-mri-datasets/04-open-mri-datasets.ipynb → code/04-open-mri-datasets.ipynb b/...n-mri-datasets/04-open-mri-datasets.ipynb → code/04-open-mri-datasets.ipynb
diff --git a/index.md b/index.md
@@ -7,7 +7,7 @@ permalink: index.html  # Is the only page that doesn't follow the pattern /:path
 The goal of this lesson is to provide an introduction to the core concepts involved in analyzing magnetic resonance imaging (MRI) data.
 It is intended for learners with no prior experience working with MRI data.
 
-The lesson will introduce different types of MRI modalities and how they can be easily organized and shared. This lesson is also a pre-requisite for [Functional MRI Data Analysis][inc-fmri] and [Diffusion MRI Data Analysis][inc-dmri], which go more in-depth into some specific MRI modalities.
+The lesson will introduce different types of MRI modalities and how they can be easily organized and shared. This lesson is also a pre-requisite for the [Structural][inc-smri], [Functional][inc-fmri] and [Diffusion][inc-dmri] MRI Data Analysis lessons, which go more in-depth into some specific MRI modalities.
 
 Over the past decade, the neuroimaging field has produced (and continues to produce) incredible amounts of data about the brain. As a result, the scientific community has developed a diverse set of tools to facilitate the access, analysis and visualization of this data. This lesson will start you on a path towards using these tools effectively in your own work.
 
@@ -27,5 +27,6 @@ To get started, follow the directions on the [Setup][lesson-setup] page to insta
 
 [swc-python]: https://swcarpentry.github.io/python-novice-inflammation
 [swc-shell]: https://swcarpentry.github.io/shell-novice
+[inc-smri]: https://carpentries-incubator.github.io/SDC-BIDS-sMRI
 [inc-fmri]: https://carpentries-incubator.github.io/SDC-BIDS-fMRI
 [inc-dmri]: https://carpentries-incubator.github.io/SDC-BIDS-dMRI
diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,6 @@
-awscli
 datalad
 matplotlib
 nibabel
 numpy
 pandas
-pybids
+pybids