fixing docker image

Author: Barthelemy-Drabczuk

.github/Dockerfile.base

@@ -22,6 +22,14 @@ WORKDIR ${HOME}/app
 
 # Copy pipeline from build context (reflects local changes; submodules in external/)
 COPY --chown=user:user . champollion_pipeline/
+# cortical_tiles/logs.py uses gitpython to record the repo HEAD commit SHA.
+# The submodule .git pointer is broken without the parent .git/modules/ tree.
+# Replace it with a minimal stub git repo so gitpython finds a valid HEAD.
+RUN rm -f champollion_pipeline/external/cortical_tiles/.git \
+    && git -C champollion_pipeline/external/cortical_tiles init \
+    && git -C champollion_pipeline/external/cortical_tiles \
+       -c user.email="build@docker" -c user.name="Docker" \
+       commit --allow-empty -m "Docker build snapshot"
 # Clone champollion_utils (separate external repository)
 RUN git clone --depth 1 -b master https://github.com/neurospin/champollion_utils.git
 

README.md

@@ -106,7 +106,10 @@ pixi run python3 src/run_cortical_tiles.py \
     --path_sk_with_hull "t1mri/default_acquisition/default_analysis/segmentation"
 ```
 
-The `input` argument is the directory containing subject folders (e.g., morphologist's output subjects directory). The `--path_to_graph` supports wildcards (`*`) for variable path segments, e.g.:
+- **`input`** — directory containing one folder per subject (e.g., morphologist's `subjects/` output). This path may be read-only (e.g., an NFS database): the script never writes to it.
+- **`output`** — derivatives parent directory. The script writes `pipeline_loop_2mm.json` here and produces sulcal region crops at `{output}/cortical_tiles-2026/crops/2mm/`.
+
+The `--path_to_graph` supports wildcards (`*`) for variable path segments, e.g.:
 
 ```bash
 --path_to_graph "t1mri/default_acquisition/*/folds/3.1"