ENH harvard oxford atlas (#132)

* EHN Harvard-Oxford atlas

* auto detec preset atlas

* Help str get the atlas automatically as well

* ADD atlas to the docker atlas download tool

* ADD changelog

* FIX add harvard-oxford to atlas download and trim down the docker file

* docker will test all default atlas

* docker artefacts should have different names, output path can be the same

* remove th0 since the coverage is too liberal and makes little sense

* can if statement run under job id?

* TEST job level if statement cannot access env

.github/workflows/docker.yml

@@ -11,6 +11,7 @@ on:
       - 'Dockerfile'
       - 'requirements.txt'
       - '.github/workflows/docker.yml'
+      - 'tools/*'
   release:
     types: [published]
 
@@ -26,8 +27,6 @@ env:
   REPO_NAME: giga_connectome
   DATA:  /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
   IMAGE: /home/runner/work/giga_connectome/giga_connectome/docker
-  IS_TAGGED: ${{ github.ref_type == 'tag' }}
-  IS_MAIN: ${{ github.ref == 'refs/heads/main' }}
 
 jobs:
   download-test-data:
@@ -70,6 +69,9 @@ jobs:
   docker-run:
     runs-on: ubuntu-latest
     needs: [download-test-data, docker-build]
+    strategy:
+      matrix:
+        atlas: ['Schaefer20187Networks', 'MIST', 'DiFuMo', 'HarvardOxfordCortical', 'HarvardOxfordCorticalSymmetricSplit', 'HarvardOxfordSubcortical']
     steps:
       - uses: actions/checkout@v4
         with:
@@ -96,13 +98,14 @@ jobs:
             /outputs \
             participant \
             -w /work \
+            --atlas ${{ matrix.atlas }} \
             --participant_label 1 \
             --reindex-bids
 
       - name: Upload output artifact
         uses: actions/upload-artifact@v4
         with:
-          name: connectome
+          name: connectome_${{ matrix.atlas }}
           path: ./outputs/
 
   docker-push:
@@ -111,6 +114,7 @@ jobs:
     defaults:
       run:
           shell: bash -el {0}
+    if: ${{ github.ref == 'refs/heads/main' || github.ref_type == 'tag' }}
     steps:
       - uses: actions/checkout@v4
         with:
@@ -128,14 +132,13 @@ jobs:
       - name: Load image
         run: docker load -i ${{ env.IMAGE }}/image.tar
       - name: Push unstable to dockerhub on tags or on main
-        if: ${{ env.IS_MAIN == 'true' || env.IS_TAGGED == 'true' }}
         run: |
           echo "Pushing unstable versions to DockerHub"
           unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable"
           docker tag "${{env.USER_NAME}}/${{env.REPO_NAME}}" "${unstable}"
           docker push "${unstable}"
       - name: Push stable release to dockerhub on tags only
-        if: ${{ env.IS_TAGGED == 'true' }}
+        if: ${{ github.ref_type == 'tag' }}
         run: |
           echo "Pushing stable and latest versions to DockerHub for latest and  ${{ github.ref_name }}"
 

Dockerfile

@@ -16,7 +16,6 @@ COPY [".", "/code"]
 
 RUN pip3 install --no-cache-dir pip==24.0 && \
     pip3 install --no-cache-dir --requirement requirements.txt && \
-    python3 -c "from templateflow.api import get; get(['MNI152NLin2009cAsym', 'MNI152NLin6Asym'])" && \
     pip3 --no-cache-dir install .
 
 ENV TEMPLATEFLOW_HOME=${TEMPLATEFLOW_HOME}

README.md

@@ -28,7 +28,7 @@ Pull from `Dockerhub` (Recommended)
 
 ```bash
 docker pull bids/giga_connectome:latest
-docker run -ti --rm --read-only bids/giga_connectome --help
+docker run -ti --rm bids/giga_connectome --help
 ```
 
 If you want to get the bleeding-edge version of the app,

docs/source/changes.md

@@ -6,13 +6,18 @@ Released MONTH YEAR
 
 ### New
 
+- [EHN] Add Harvard-Oxford atlas. (@htwangtw) [#117](https://github.com/bids-apps/giga_connectome/issues/117)
 - [DOCS] Improved documentation on using customised configuration files. (@htwangtw)
 - [ENH] use logger instead of print statements. (@Remi-Gau)
 
 ### Fixes
 
 - [FIX] Bump nilearn version to 0.10.2 to fix issues [#26](https://github.com/bids-apps/giga_connectome/issues/26) and [#27](https://github.com/bids-apps/giga_connectome/issues/27). (@Remi-Gau)
 
+### Enhancements
+
+- [ENH] Reduce the docker image size. (@htwangtw)
+
 ### Changes
 
 - [ENH] Make output more BIDS compliant. (@Remi-Gau)

giga_connectome/atlas.py

@@ -15,9 +15,6 @@
 
 gc_log = gc_logger()
 
-
-PRESET_ATLAS = ["DiFuMo", "MIST", "Schaefer20187Networks"]
-
 ATLAS_CONFIG_TYPE = TypedDict(
     "ATLAS_CONFIG_TYPE",
     {
@@ -153,6 +150,12 @@ def resample_atlas_collection(
     return resampled_atlases
 
 
+def get_atlas_labels() -> List[str]:
+    """Get the list of available atlas labels."""
+    atlas_dir = resource_filename("giga_connectome", "data/atlas")
+    return [p.stem for p in Path(atlas_dir).glob("*.json")]
+
+
 def _check_altas_config(
     atlas: str | Path | dict[str, Any]
 ) -> ATLAS_CONFIG_TYPE:
@@ -174,8 +177,10 @@ def _check_altas_config(
         atlas configuration not containing the correct keys.
     """
     # load the file first if the input is not already a dictionary
+    atlas_dir = resource_filename("giga_connectome", "data/atlas")
+    preset_atlas = [p.stem for p in Path(atlas_dir).glob("*.json")]
     if isinstance(atlas, (str, Path)):
-        if atlas in PRESET_ATLAS:
+        if atlas in preset_atlas:
             config_path = Path(
                 resource_filename(
                     "giga_connectome", f"data/atlas/{atlas}.json"

giga_connectome/data/atlas/HarvardOxfordCortical.json

@@ -0,0 +1,14 @@
+{
+    "name": "HarvardOxfordCortical",
+    "parameters": {
+        "atlas": "HOCPA",
+        "template": "MNI152NLin2009cAsym",
+        "resolution": "02",
+        "suffix": "dseg"
+    },
+    "desc": [
+        "th25",
+        "th50"
+    ],
+    "templateflow_dir" : null
+}

giga_connectome/data/atlas/HarvardOxfordCorticalSymmetricSplit.json

@@ -0,0 +1,14 @@
+{
+    "name": "HarvardOxfordCorticalSymmetricSplit",
+    "parameters": {
+        "atlas": "HOCPAL",
+        "template": "MNI152NLin2009cAsym",
+        "resolution": "02",
+        "suffix": "dseg"
+    },
+    "desc": [
+        "th25",
+        "th50"
+    ],
+    "templateflow_dir" : null
+}

giga_connectome/data/atlas/HarvardOxfordSubcortical.json

@@ -0,0 +1,14 @@
+{
+    "name": "HarvardOxfordSubcortical",
+    "parameters": {
+        "atlas": "HOSPA",
+        "template": "MNI152NLin2009cAsym",
+        "resolution": "02",
+        "suffix": "dseg"
+    },
+    "desc": [
+        "th25",
+        "th50"
+    ],
+    "templateflow_dir" : null
+}

giga_connectome/run.py

@@ -6,6 +6,9 @@
 
 from giga_connectome import __version__
 from giga_connectome.workflow import workflow
+from giga_connectome.atlas import get_atlas_labels
+
+preset_atlas = get_atlas_labels()
 
 
 def global_parser() -> argparse.ArgumentParser:
@@ -58,7 +61,7 @@ def global_parser() -> argparse.ArgumentParser:
     parser.add_argument(
         "--atlas",
         help="The choice of atlas for time series extraction. Default atlas "
-        "choices are: 'Schaefer20187Networks, 'MIST', 'DiFuMo'. User can pass "
+        f"choices are: {preset_atlas}. User can pass "
         "a path to a json file containing configuration for their own choice "
         "of atlas. The default is 'Schaefer20187Networks'.",
         default="Schaefer20187Networks",

giga_connectome/tests/test_atlas.py

@@ -4,3 +4,5 @@
 def test_load_atlas_setting():
     atlas_config = load_atlas_setting("Schaefer20187Networks")
     assert atlas_config["name"] == "Schaefer20187Networks"
+    atlas_config = load_atlas_setting("HarvardOxfordCortical")
+    assert atlas_config["name"] == "HarvardOxfordCortical"

tools/download_templates.py

@@ -18,11 +18,13 @@
 
 def fetch_tpl_atlas() -> None:
     """Download datasets from templateflow."""
-    atlases = ["Schaefer2018", "DiFuMo"]
+    atlases = ["Schaefer2018", "DiFuMo", "HOSPA", "HOCPA", "HOCPAL"]
     for atlas in atlases:
         tf_path = tf.api.get("MNI152NLin2009cAsym", atlas=atlas)
         if isinstance(tf_path, list) and len(tf_path) > 0:
             gc_log.info(f"{atlas} exists.")
+        else:
+            gc_log.error(f"{atlas} does not exist.")
     # download MNI grey matter template
     tf.api.get("MNI152NLin2009cAsym", label="GM")