diff --git a/.github/workflows/bump_version.yml b/.github/workflows/bump_version.yml
index 0ab3e332..74f6cfaf 100644
--- a/.github/workflows/bump_version.yml
+++ b/.github/workflows/bump_version.yml
@@ -1,13 +1,16 @@
+---
 name: Bump version
 on:
   push:
     branches:
       - master
+
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - name: Checkout main branch
+        uses: actions/checkout@v4
 
       - name: Update changelog
         uses: release-drafter/release-drafter@v5
@@ -15,6 +18,9 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # Can replace the below with (until pipeline description) with
+      # khanlab/actions/.github/workflows/workflow-version_task-semverGithub.yml
+      # after adding PAT token
       - name: Get previous release version
         run: |
           echo "PREV_VER=$(cat pyproject.toml | grep -o -E '(version\s=\s)([[:punct:]])([0-9]+\.[0-9]+\.[0-9]+.+)([[:punct:]])' | cut -d ' ' -f 3 | tr -d '"')" >> $GITHUB_ENV
@@ -35,28 +41,27 @@ jobs:
         run: |
           echo "NEW_BUMP=$(($BUMP_VER + 1))" >> $GITHUB_ENV
 
-      - name: Update version in pyproject
-        uses: jacobtomlinson/gha-find-replace@master
+      - name: Update version in pyproject.toml
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'pyproject.toml'
+          include: "pyproject.toml"
           find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version = "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
       - name: Update version in pipeline_description (not actually used)
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/pipeline_description.json'
+          include: "hippunfold/pipeline_description.json"
           find: '"Version": "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: '"Version": "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
       - name: Update version in config/snakebids.yml
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/config/snakebids.yml'
+          include: "hippunfold/config/snakebids.yml"
           find: 'version: "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version: "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
- 
       - name: Commit updates
         env:
           SNAKEBIDS_VERSION: ${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}
@@ -66,10 +71,7 @@ jobs:
           git diff-index --quiet HEAD || git commit -m "Bump version to $SNAKEBIDS_VERSION" -a
 
       - name: Push changes
-        uses: ad-m/github-push-action@master
+        uses: ad-m/github-push-action@v0.8.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           tags: false
-
-
-
diff --git a/.github/workflows/dags.yml b/.github/workflows/dags.yml
index e3f27d3d..4be2bc88 100644
--- a/.github/workflows/dags.yml
+++ b/.github/workflows/dags.yml
@@ -1,31 +1,26 @@
+---
 name: Generate DAG visualizations
-
 on:
   workflow_dispatch:
     inputs:
-      author:
-        description: "Author"
-        required: true
-        default: "github-actions[bot] (user publishing release)"
-      date:
-        description: "Date"
-        required: true
-        default: "YYYY-MM-DD"
       comments:
         description: "Comments"
 
 jobs:
   generate_dag:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
 
     steps:
       - name: Print author
         run: |
-          echo "Author: ${{ github.event.inputs.author }}"
-          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Author: ${{ github.triggering_actor }}"
           echo "Comments: ${{ github.event.inputs.comments }}"
 
-      - uses: actions/checkout@master
+      - name: Checkout main branch
+        uses: actions/checkout@v3
         with:
           ref: refs/heads/master
 
@@ -33,34 +28,32 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install non-python dependencies
         run: |
           sudo apt-get install -y graphviz-dev graphviz
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install snakebids
 
-      - name: Set-up env for hippunfold 
+      - name: Set-up env for hippunfold
         run: |
           echo "HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models" >> $GITHUB_ENV
           echo "HIPPUNFOLD=./hippunfold/run.py" >> $GITHUB_ENV
+
       - name: Generate rulegraph single T2w bids
         run: |
           $HIPPUNFOLD test_data/bids_singleT2w test_out participant -np --modality T2w --rulegraph | dot -Tsvg > docs/images/rulegraph_T2w.svg
 
       - name: Commit updates
-        env:
-          LATEST_VERSION: ${{ steps.release-drafter.outputs.name }}
         run: |
           git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --local user.name "github-actions[bot]"
-          git diff-index --quiet HEAD || git add docs/images || commit -m "Add updated dags [skip ci]" 
+          git diff-index --quiet HEAD || git add docs/images || commit -m "Add updated dags [skip ci]"
 
       - name: Push changes
-        uses: ad-m/github-push-action@master
+        uses: ad-m/github-push-action@v0.8.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-
-
-
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index fb1fcfe9..f832ef4a 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -1,16 +1,8 @@
+---
 name: Deploy workflow
-
 on:
   workflow_dispatch:
     inputs:
-      author:
-        description: "Author"
-        required: true
-        default: "github-actions[bot] (user publishing release)"
-      date:
-        description: "Date"
-        required: true
-        default: "YYYY-MM-DD"
       comments:
         description: "Comments"
       branch:
@@ -25,11 +17,10 @@ jobs:
     steps:
       - name: Print author
         run: |
-          echo "Author: ${{ github.event.inputs.author }}"
-          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Author: ${{ github.triggering_actor }}"
           echo "Comments: ${{ github.event.inputs.comments }}"
 
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.inputs.branch }}
 
@@ -37,10 +28,13 @@ jobs:
         uses: release-drafter/release-drafter@v5
         id: release-drafter
         with:
-          commitish: ${{ github.event.inputs.branch }}        
+          commitish: ${{ github.event.inputs.branch }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # Can replace the below with (until pipeline description) with
+      # khanlab/actions/.github/workflows/workflow-version_task-publishGithub.yml
+      # after adding PAT token
       - name: Set new release version
         env:
           RD_RELEASE: ${{ steps.release-drafter.outputs.name }}
@@ -52,27 +46,26 @@ jobs:
           fi
 
       - name: Update version in pyproject.toml
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'pyproject.toml'
+          include: "pyproject.toml"
           find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version = "${{ env.NEW_RELEASE }}"'
 
       - name: Update version in pipeline_description (not actually used)
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/pipeline_description.json'
+          include: "hippunfold/pipeline_description.json"
           find: '"Version": "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: '"Version": "${{ env.NEW_RELEASE }}"'
 
       - name: Update version in config/snakebids.yml
-        uses: jacobtomlinson/gha-find-replace@master
+        uses: jacobtomlinson/gha-find-replace@v3
         with:
-          include: 'hippunfold/config/snakebids.yml'
+          include: "hippunfold/config/snakebids.yml"
           find: 'version: "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version: "${{ env.NEW_RELEASE }}"'
 
- 
       - name: Commit updates
         env:
           LATEST_VERSION: ${{ env.NEW_RELEASE }}
@@ -82,7 +75,7 @@ jobs:
           git diff-index --quiet HEAD || git commit -m "Bump version to $LATEST_VERSION" -a
 
       - name: Push changes
-        uses: ad-m/github-push-action@master
+        uses: ad-m/github-push-action@v0.8.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
 
@@ -92,5 +85,3 @@ jobs:
           publish: true
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-
diff --git a/.github/workflows/manual_release_drafter.yml b/.github/workflows/manual_release_drafter.yml
index 1d7294f4..2a8a214c 100644
--- a/.github/workflows/manual_release_drafter.yml
+++ b/.github/workflows/manual_release_drafter.yml
@@ -1,12 +1,8 @@
+---
 name: Manual release-drafter update
-
 on:
   workflow_dispatch:
     inputs:
-      author:
-        description: "Author"
-        required: true
-        default: "github-actions[bot] (user publishing release)"
       comments:
         description: "Update release drafter notes"
 
@@ -16,11 +12,11 @@ jobs:
     steps:
       - name: Print workflow information
         run: |
-          echo "Author: ${{ github.event.inputs.author }}"
-          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Author: ${{ github.triggering_actor }}"
           echo "Comments: ${{ github.event.inputs.comments }}"
 
-      - uses: actions/checkout@master
+      - name: Checkout main branch
+        uses: actions/checkout@v4
 
       - name: Update changelog
         uses: release-drafter/release-drafter@v5
diff --git a/.github/workflows/push_container.yml b/.github/workflows/push_container.yml
index f0acba28..3b2c3388 100644
--- a/.github/workflows/push_container.yml
+++ b/.github/workflows/push_container.yml
@@ -1,53 +1,18 @@
+---
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
 
 name: Publish Docker image
-
-on: 
+on:
   workflow_dispatch:
   release:
     types: [published]
 
 jobs:
   push_to_registries:
-    name: Push Docker image to multiple registries
-    runs-on: ubuntu-latest
-    permissions:
-      packages: write
-      contents: read
-    steps:
-      - name: Check out the repo
-        uses: actions/checkout@master
-      
-      - name: Log in to Docker Hub
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-      
-      - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-      
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v4
-        with:
-          images: |
-            ${{ github.repository }}
-            ghcr.io/${{ github.repository }}
-          flavor: |
-            latest=auto
-      
-      - name: Build and push Docker images
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
-        with:
-          context: .
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+    uses: khanlab/actions/.github/workflows/workflow-release_task-deployDocker.yml@v0.3.2
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml
index af0efacb..88734d54 100644
--- a/.github/workflows/python-testing.yml
+++ b/.github/workflows/python-testing.yml
@@ -1,189 +1,136 @@
+---
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
-
+name: Lint and test workflow
 on:
   push:
   workflow_dispatch:
-#    branches: [ main ]
-#  pull_request:
-#    branches: [ main ]
 
 jobs:
-  
   quality:
     runs-on: ubuntu-latest
+
     steps:
-      - name: Clone repo
-        uses: actions/checkout@master
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.8'
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-3.8
-          restore-keys: ${{ runner.os }}-pip-3.8
       - name: Install non-python dependencies
         run: |
           sudo apt-get install -y graphviz-dev
-      #----------------------------------------------
-      #  -----  install & configure poetry  -----
-      #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: Disable Poetry modern installation
-        run: |
-          poetry config installer.modern-installation false
-      #----------------------------------------------
-      #----------------------------------------------
-      #       load cached venv if cache exists
-      #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v3
+
+      - name: Setup Python environment
+        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.2
         with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-3.8
-      #----------------------------------------------
-      # install dependencies if cache does not exist
-      #----------------------------------------------
-      - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
-      #----------------------------------------------
-      # install your root project, if required
-      #----------------------------------------------
-      - name: Install library
-        run: poetry install --no-interaction
-
-      #----------------------------------------------
-      #       run python style checks
-      #----------------------------------------------
+          python-version: "3.9"
+
       - name: isort
         run: poetry run isort hippunfold/*.py -c
+
       - name: Black
         run: poetry run black hippunfold --check
+
       - name: snakefmt
         run: poetry run snakefmt hippunfold --check
- 
-  test:
 
+  test:
     runs-on: ubuntu-latest
-    needs: [ 'quality'  ]
+    needs: ["quality"]
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ["3.7", "3.8", "3.9"]
+
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ matrix.python-version }}
-        restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
-    - name: Install non-python dependencies
-      run: |
-        sudo apt-get install -y graphviz-dev
-    #----------------------------------------------
-    #  -----  install & configure poetry  -----
-    #----------------------------------------------
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-    - name: Disable Poetry modern installation
-      run: |
-        poetry config installer.modern-installation false
-    #----------------------------------------------
-    #       load cached venv if cache exists
-    #----------------------------------------------
-    - name: Load cached venv
-      id: cached-poetry-dependencies
-      uses: actions/cache@v3
-      with:
-        path: .venv
-        key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-${{ matrix.python-version }}
-    #----------------------------------------------
-    # install dependencies if cache does not exist
-    #----------------------------------------------
-    - name: Install dependencies
-      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      run: poetry install --no-interaction --no-root
-    #----------------------------------------------
-    # install your root project, if required
-    #----------------------------------------------
-    - name: Install library
-      run: poetry install --no-interaction
-    - name: Set-up env for hippunfold 
-      run: |
-        echo "HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models" >> $GITHUB_ENV
-    - name: Test single T2w bids
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w
-    - name: Test running on existing folder
-      run: |
-        mkdir test_newout
-        poetry run hippunfold test_data/bids_singleT2w test_newout participant -np --modality T2w
-    - name: Test single T2w bids, right hemi
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R
-    - name: Test single T2w bids, left hemi
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L
-    - name: Test multiple T2w bids
-      run: |
-        poetry run hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w
-    - name: Test T1w bids
-      run: |
-        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w
-    - name: Test hipp b500 bids
-      run: |
-        poetry run hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500
-    - name: Test T1w multi-session/longitudinal bids
-      run: |
-        poetry run hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w
-    - name: Test single T2w multi-session/longitudinal bids
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w
-    - name: Test manual seg T2w bids
-      run: |
-        poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w
-    - name: Test cropseg bids, with path override
-      run: |
-        poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
-    - name: Test cropseg bids, with path override, left hemi
-      run: | 
-        poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
-    - name: Test T2w with T1w template registration
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template
-    - name: Test T2w with T1w output space 
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w
-    - name: Test modality T2w with myelin map
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --generate-myelin-map
-    - name: Test modality T1w with myelin map
-      run: |
-        poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T1w --generate-myelin-map
-    - name: Test modality T1w with magdeburg atlas
-      run: |
-        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas magdeburg
-    - name: Test modality T1w with freesurfer atlas
-      run: |
-        poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer
+    
+      - name: Install non-python dependencies
+        run: |
+          sudo apt-get install -y graphviz-dev
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup Python environments
+        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.2
+        with:
+          python-version: ${{ matrix.python-version }}
+          install-library: true
+
+      - name: Setup env for hippunfold
+        run: |
+          echo "HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models" >> $GITHUB_ENV
+
+      - name: Test single T2w bids
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w
+
+      - name: Test running on existing folder
+        run: |
+          mkdir test_newout
+          poetry run hippunfold test_data/bids_singleT2w test_newout participant -np --modality T2w
+
+      - name: Test single T2w bids, right hemi
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R
 
+      - name: Test single T2w bids, left hemi
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L
+
+      - name: Test multiple T2w bids
+        run: |
+          poetry run hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w
+
+      - name: Test T1w bids
+        run: |
+          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w
+
+      - name: Test hipp b500 bids
+        run: |
+          poetry run hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500
 
+      - name: Test T1w multi-session/longitudinal bids
+        run: |
+          poetry run hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w
+
+      - name: Test single T2w multi-session/longitudinal bids
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w
 
+      - name: Test manual seg T2w bids
+        run: |
+          poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w
 
+      - name: Test cropseg bids, with path override
+        run: |
+          poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+
+      - name: Test cropseg bids, with path override, left hemi
+        run: |
+          poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
 
+      - name: Test T2w with T1w template registration
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template
+
+      - name: Test T2w with T1w output space
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w
+
+      - name: Test modality T2w with myelin map
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --generate-myelin-map
+
+      - name: Test modality T1w with myelin map
+        run: |
+          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T1w --generate-myelin-map
+
+      - name: Test modality T1w with magdeburg atlas
+        run: |
+          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas magdeburg
+
+      - name: Test modality T1w with freesurfer atlas
+        run: |
+          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer
+
+      - name: Test modality T1w with bigbrain and freesurfer atlas
+        run: |
+          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas bigbrain freesurfer
diff --git a/README.md b/README.md
index fcdc6d03..37fb51d7 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
 [![Documentation Status](https://readthedocs.org/projects/hippunfold/badge/?version=latest)](https://hippunfold.readthedocs.io/en/latest/?badge=latest)
 ![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/hippunfold)
 ![Version](https://img.shields.io/github/v/tag/khanlab/hippunfold?label=version)
+<img align="right" width="200" src="https://github.com/khanlab/hippunfold/assets/25106300/0c16d33e-893a-4ac3-b127-21fa843823d5">
 
 **Full Documentation:**  [here](https://hippunfold.readthedocs.io/en/latest/?badge=latest)
 
@@ -8,7 +9,6 @@
 
 This tool aims to automatically model the topological folding structure
 of the human hippocampus, and computationally unfold it.
-https://raw.githubusercontent.com//khanlab/hippunfold/master/docs/images/subfields_foldunfold.png
 ![Hippo Fold Unfold](https://raw.githubusercontent.com//khanlab/hippunfold/master/docs/images/subfields_foldunfold.png)
 
 This is especially useful for:
@@ -24,7 +24,7 @@ Major changes include the addition of unfolded space registration to a reference
 
 *Note: this replaces the default workflow, however you can revert to the legacy workflow, disabling unfolded space registration, by setting `--atlas bigbrain` or `--no-unfolded-reg`*
 
-Read more in our [preprinted manuscript](https://www.biorxiv.org/content/10.1101/2023.03.30.534978v1)
+Read more in our [ manuscript](https://doi.org/10.7554/eLife.88404.3)
 
 Also the ability to specify a new **experimental** UNet model that is contrast-agnostic using [synthseg](https://github.com/BBillot/SynthSeg) and trained using more detailed segmentations. This generally produces more detailed results but has not been extensively tested yet. 
 
@@ -45,11 +45,22 @@ For plotting, mapping fMRI, DWI or other data, and manipulating surfaces, see [h
 
 For statistical testing (spin tests) in unfolded space, see [here](https://github.com/Bradley-Karat/Hippo_Spin_Testing)
 
-## Relevant papers:
-- DeKraker, J., Palomero-Gallagher, N., Kedo, O., Ladbon-Bernasconi, N., Muenzing, S. E., Axer, M., ... & Evans, A. C. (2023). Evaluation of surface-based hippocampal registration using ground-truth subfield definitions. bioRxiv, 2023-03. [link](https://www.biorxiv.org/content/10.1101/2023.03.30.534978v1)
+## Publications
+
+### HippUnfold methods paper
+
 - DeKraker, J., Haast, R. A., Yousif, M. D., Karat, B., Lau, J. C., Köhler, S., & Khan, A. R. (2022). Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold. Elife, 11, e77945. [link](https://doi.org/10.7554/eLife.77945)
-- DeKraker J, Ferko KM, Lau JC, Köhler S, Khan AR. Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. Neuroimage. 2018 Feb 15;167:408-418. doi: 10.1016/j.neuroimage.2017.11.054. Epub 2017 Nov 23. PMID: 29175494. [link](https://pubmed.ncbi.nlm.nih.gov/29175494/)
-- DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S. Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. Neuroimage. 2020 Feb 1;206:116328. doi: 10.1016/j.neuroimage.2019.116328. Epub 2019 Nov 1. PMID: 31682982. [link](https://pubmed.ncbi.nlm.nih.gov/31682982/)
+  -  **Please cite this if you use any version of HippUnfold)**
+  
+### Unfolded space registration and multihist7 atlas
+- DeKraker Jordan, Palomero-Gallagher Nicola, Kedo Olga, Ladbon-Bernasconi Neda, Muenzing Sascha E.A., Axer Markus, Amunts Katrin, Khan Ali R., Bernhardt Boris, Evans Alan C. (2023) Evaluation of surface-based hippocampal registration using ground-truth subfield definitions eLife 12:RP88404 [link](https://doi.org/10.7554/eLife.88404.3)
+  -  **Please cite this if you use HippUnfold version >= 1.3.0)**
+
+### Commentary on surface-based hippocampal segmentation
 - DeKraker J, Köhler S, Khan AR. Surface-based hippocampal subfield segmentation. Trends Neurosci. 2021 Nov;44(11):856-863. doi: 10.1016/j.tins.2021.06.005. Epub 2021 Jul 22. PMID: 34304910. [link](https://pubmed.ncbi.nlm.nih.gov/34304910/)
 
+### Related papers
 
+- DeKraker J, Ferko KM, Lau JC, Köhler S, Khan AR. Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. Neuroimage. 2018 Feb 15;167:408-418. doi: 10.1016/j.neuroimage.2017.11.054. Epub 2017 Nov 23. PMID: 29175494. [link](https://pubmed.ncbi.nlm.nih.gov/29175494/)
+- DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S. Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. Neuroimage. 2020 Feb 1;206:116328. doi: 10.1016/j.neuroimage.2019.116328. Epub 2019 Nov 1. PMID: 31682982. [link](https://pubmed.ncbi.nlm.nih.gov/31682982/)
+- Karat BG, DeKraker J, Hussain U, Köhler S, Khan AR. Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI. Hum Brain Mapp. 2023 Nov;44(16):5485-5503. Epub 2023 Aug 24. PMID: 37615057; PMCID: PMC10543110.[link](https://doi.org/10.1002/hbm.26461)
diff --git a/docs/requirements.txt b/docs/requirements.txt
index d4962a84..713e48d4 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -4,3 +4,4 @@ sphinx_rtd_theme>=1.0.0
 snakebids>=0.4.0
 myst-parser
 sphinxcontrib.asciinema
+pulp<2.8.0
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
index 65ce94c9..537722da 100644
--- a/hippunfold/config/snakebids.yml
+++ b/hippunfold/config/snakebids.yml
@@ -128,7 +128,7 @@ parse_args:
   --version:
     help: 'Print the version of HippUnfold'
     action: version
-    version: "1.4.2-pre.29"
+    version: "1.4.2-pre.33"
 
 
   --modality:
diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json
index a91e1e09..98c8da8f 100644
--- a/hippunfold/pipeline_description.json
+++ b/hippunfold/pipeline_description.json
@@ -5,7 +5,7 @@
     "GeneratedBy": [
         {
             "Name": "hippunfold",
-            "Version": "1.4.2-pre.29",
+            "Version": "1.4.2-pre.33",
             "CodeURL": "https://github.com/khanlab/hippunfold",
             "Author": "Jordan DeKraker & Ali Khan",
             "AuthorEmail": "ali.khan@uwo.ca"
diff --git a/pyproject.toml b/pyproject.toml
index 0d4d4527..a5c9fe54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hippunfold"
-version = "1.4.2-pre.29"
+version = "1.4.2-pre.33"
 description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)"
 authors = ["Jordan DeKraker & Ali Khan <alik@robarts.ca>"]