Reformat AtlasPack into a BIDS dataset and fix ANTS and AFNI (#35)

* Reformat AtlasPack into a BIDS dataset.

* Update Dockerfile

Dockerfile

@@ -11,9 +11,6 @@ COPY --from=atlaspack /AtlasPack/tpl-MNI152NLin6Asym_*.nii.gz /AtlasPack/
 COPY --from=atlaspack /AtlasPack/atlas-4S*.tsv /AtlasPack/
 COPY --from=atlaspack /AtlasPack/*.json /AtlasPack/
 
-# Write dataset_description.json
-RUN echo '{"Name": "AtlasPack", "BIDSVersion": "1.0.0", "DatasetType": "atlas"}' >> /AtlasPack/dataset_description.json
-
 # Install basic libraries
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -114,12 +111,9 @@ RUN apt-get update -qq \
 | tar -xz -C /opt/afni-latest --strip-components 1
 
 # Configure AFNI
-ENV AFNI_MODELPATH="/opt/afni-latest/models" \
-    AFNI_IMSAVE_WARNINGS="NO" \
-    AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
-    AFNI_PLUGINPATH="/opt/afni-latest/plugins"
-
-ENV PATH="/opt/afni-latest/bin:$PATH"
+ENV PATH="$PATH:/opt/afni-latest" \
+    AFNI_INSTALLDIR=/opt/afni-latest \
+    AFNI_IMSAVE_WARNINGS=NO
 
 RUN echo "Downloading C3D ..." \
     && mkdir /opt/c3d \
@@ -170,7 +164,7 @@ RUN mkdir -p $ANTSPATH && \
     curl -sSL "https://github.com/ANTsX/ANTs/releases/download/v2.5.3/ants-2.5.3-ubuntu-22.04-X64-gcc.zip" -o /tmp/ants.zip && \
     unzip /tmp/ants.zip -d $ANTSPATH && \
     rm /tmp/ants.zip
-ENV PATH=$ANTSPATH:$PATH
+ENV PATH=/usr/lib/ants/ants-2.5.3/bin:$PATH
 
 # Install SVGO
 RUN npm install -g svgo
@@ -200,6 +194,10 @@ RUN python fetch_templates.py && \
     find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
     find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
 
+# Reformat AtlasPack into a BIDS dataset
+COPY scripts/fix_atlaspack.py fix_atlaspack.py
+RUN python fix_atlaspack.py && rm fix_atlaspack.py
+
 # Install pandoc (for HTML/LaTeX reports)
 RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
     dpkg -i pandoc-2.2.2.1-1-amd64.deb && \

scripts/fix_atlaspack.py

@@ -0,0 +1,51 @@
+"""Convert the AtlasPack folder into a BIDS dataset."""
+
+import json
+import os
+import re
+import shutil
+
+if __name__ == "__main__":
+    # Where all the files are located
+    in_dir = "/AtlasPack"
+
+    with open(os.path.join(in_dir, "dataset_description.json"), "w") as fo:
+        json.dump(
+            {"Name": "AtlasPack", "BIDSVersion": "1.9.0", "DatasetType": "atlas"},
+            fo,
+        )
+
+    # Define patterns and corresponding target formats
+    patterns = [
+        (r"atlas-([a-zA-Z0-9+]+)_dseg.tsv", r"atlas-\1/atlas-\1_dseg.tsv"),
+        (
+            r"tpl-MNI152NLin6Asym_atlas-([a-zA-Z0-9+]+)_res-01_dseg.nii.gz",
+            r"atlas-\1/atlas-\1_space-MNI152NLin6Asym_res-01_dseg.nii.gz",
+        ),
+        (
+            r"tpl-fsLR_atlas-([a-zA-Z0-9+]+)_den-91k_dseg.dlabel.nii",
+            r"atlas-\1/atlas-\1_space-fsLR_den-91k_dseg.dlabel.nii",
+        ),
+        (
+            r"tpl-MNI152NLin6Asym_atlas-([a-zA-Z0-9+]+)_dseg.json",
+            r"atlas-\1/atlas-\1_space-MNI152NLin6Asym_res-01_dseg.json",
+        ),
+        (
+            r"tpl-fsLR_atlas-([a-zA-Z0-9+]+)_dseg.json",
+            r"atlas-\1/atlas-\1_space-fsLR_den-91k_dseg.json",
+        ),
+    ]
+
+    for pattern, target_format in patterns:
+        files = [f for f in os.listdir(in_dir) if re.search(pattern, f)]
+        for filename in files:
+            atlas_name = re.findall(pattern, filename)[0]
+            target_dir = os.path.join(in_dir, f"atlas-{atlas_name}")
+            target_path = os.path.join(in_dir, target_format.replace(r"\1", atlas_name))
+
+            # Create target directory if it doesn't exist
+            os.makedirs(target_dir, exist_ok=True)
+
+            # Move and rename the file
+            shutil.move(os.path.join(in_dir, filename), target_path)
+            print(f"Moved {filename} to {target_path}")