Merge pull request #1 from yibeichan/main

 ANTs BIDS App Implementation

Author: yibeichan

.github/workflows/ci.yml

@@ -0,0 +1,29 @@
+name: CI/CD
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install pytest pytest-cov
+    - name: Run tests
+      run: |
+        pytest --cov=src tests/ 

.gitignore

@@ -3,6 +3,7 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+data/
 # C extensions
 *.so
 
@@ -31,6 +32,7 @@ MANIFEST
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
+AGENTS.md
 
 # Installer logs
 pip-log.txt
@@ -172,3 +174,13 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+# Claude Code guidance file
+CLAUDE.md
+
+# Container images
+*.sif
+*.simg
+
+# Internal documentation and team files
+internal/

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "src/ants_seg_to_nidm"]
+	path = src/ants_seg_to_nidm
+	url = https://github.com/yibeichan/ants_seg_to_nidm.git
+	branch = feature/link-ants-acquisition

Dockerfile

@@ -0,0 +1,92 @@
+FROM ubuntu:22.04
+
+# Set non-interactive frontend for apt-get
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        python3 \
+        python3-pip \
+        python3-dev \
+        wget \
+        curl \
+        unzip \
+        git \
+        gcc \
+        g++ \
+        cmake \
+        build-essential \
+        libgomp1 \
+        ca-certificates && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Python packages
+RUN pip3 install --no-cache-dir \
+    numpy \
+    nibabel \
+    pandas \
+    pybids \
+    nipype \
+    antspyx
+
+# Create directory for templates with proper permissions
+RUN mkdir -p /opt/data && chmod 755 /opt/data
+
+# Download OASIS templates and atlases
+WORKDIR /opt/data
+
+# Download OASIS-30 Atropos template
+RUN wget -q https://files.osf.io/v1/resources/ej52r/providers/osfstorage/5e8251d20f59a8001ae648c3/?zip= \
+    -O OASIS-30_Atropos_template.zip && \
+    unzip -q OASIS-30_Atropos_template.zip && \
+    rm OASIS-30_Atropos_template.zip && \
+    chmod -R 755 /opt/data/OASIS-30_Atropos_template
+
+# Download OASIS-TRT-20 atlases for joint label fusion
+RUN wget -q https://files.osf.io/v1/resources/ej52r/providers/osfstorage/5e825d0f2301130197e6a15e/?zip= \
+    -O OASIS-TRT-20.zip && \
+    unzip -q OASIS-TRT-20.zip && \
+    rm OASIS-TRT-20.zip && \
+    chmod -R 755 /opt/data/OASIS-TRT-20_*
+
+# Create app directory with proper permissions
+RUN mkdir -p /app && chmod 755 /app
+WORKDIR /app
+
+# Copy application code
+COPY setup.py /app/
+COPY src/ /app/src/
+COPY README.md /app/
+
+# Install the application and NIDM conversion toolkit
+RUN pip3 install -e . && \
+    pip3 install -e src/ants_seg_to_nidm && \
+    pip3 install -r src/ants_seg_to_nidm/requirements.txt && \
+    chmod -R 755 /app
+
+# Set environment variables
+ENV ANTSPATH=/usr/local/bin
+ENV PATH=/usr/local/bin:$PATH
+ENV ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+
+# Create work directory for temporary files with world-writable permissions
+RUN mkdir -p /work && chmod 777 /work
+ENV TMPDIR=/work
+ENV TEMP=/work
+ENV TMP=/work
+
+# Create entrypoint script with proper permissions
+RUN echo '#!/bin/bash\nexec ants-bidsapp "$@"' > /entrypoint.sh && \
+    chmod 755 /entrypoint.sh
+
+# Ensure all installed binaries are executable
+RUN chmod -R 755 /usr/local/bin || true
+
+# Set a non-root user (but allow running as any UID/GID)
+# This helps with permission issues in HPC environments
+RUN echo "ALL ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers && \
+    chmod 666 /etc/passwd /etc/group || true
+
+ENTRYPOINT ["/entrypoint.sh"]

README.md

@@ -1 +1,138 @@
-# ants_bidsapp
+# ANTs BIDS App
+
+A BIDS App for ANTs-based brain segmentation with NIDM outputs.
+
+## Overview
+
+This BIDS App provides a standardized way to run ANTs-based brain segmentation on BIDS-formatted datasets. It includes preprocessing steps, segmentation, and generates NIDM-compatible outputs for better reproducibility and sharing of results.
+
+## Features
+
+- BIDS-compliant input/output
+- ANTs-based brain segmentation
+- N4 bias field correction
+- Brain extraction
+- Tissue segmentation
+- NIDM-compatible outputs
+- Docker and Singularity support
+
+## Installation
+
+### Container Images
+
+Pre-built images will be available once the app is published to Docker Hub. For now, please build from source (see below).
+
+### From Source
+
+```bash
+git clone https://github.com/ReproNim/ants-bidsapp.git
+cd ants-bidsapp
+pip install -e .
+```
+
+### Building Containers from Source
+
+This BIDS App follows standard BIDS Apps practices with a Dockerfile as the primary container definition. For HPC environments without Docker, we also provide a native Singularity definition file.
+
+#### Building with Docker (on systems with Docker installed)
+
+```bash
+# Using the setup.py helper script
+python setup.py docker
+
+# Or directly with Docker
+docker build -t ants-bidsapp:latest .
+
+# Save for transfer to HPC (if needed)
+docker save ants-bidsapp:latest -o ants-bidsapp.tar
+```
+
+#### Building with Singularity/Apptainer (for HPC environments)
+
+```bash
+# Direct build from Singularity definition file
+# The --fakeroot flag is required on HPC systems without root access
+apptainer build --fakeroot ants-bidsapp.sif Singularity
+
+# Or using the setup.py helper
+python setup.py singularity
+```
+
+#### Converting Docker to Singularity
+
+If you have a Docker image (either built locally or from a tar file):
+
+```bash
+# From a saved Docker tar file
+singularity build ants-bidsapp.sif docker-archive://ants-bidsapp.tar
+
+# From local Docker daemon (requires Docker)
+singularity build ants-bidsapp.sif docker-daemon://ants-bidsapp:latest
+```
+
+## Usage
+
+### Basic Usage
+
+```bash
+ants-bidsapp bids_dir output_dir participant --participant-label 01
+```
+
+### Advanced Options
+
+```bash
+ants-bidsapp bids_dir output_dir participant \
+  --participant-label 01 \
+  --session-label pre \
+  --modality T1w \
+  --prob-threshold 0.5 \
+  --num-threads 4 \
+  --verbose
+```
+
+### Command-line Arguments
+
+- `bids_dir`: Path to the BIDS dataset
+- `output_dir`: Path where outputs will be stored
+- `analysis_level`: Level of the analysis (participant)
+- `--participant-label`: Label(s) of the participant(s) to analyze
+- `--session-label`: Label(s) of the session(s) to analyze
+- `--modality`: Imaging modality to process (default: T1w)
+- `--prob-threshold`: Probability threshold for binary mask creation (default: 0.5)
+- `--priors`: Paths to prior probability maps for segmentation
+- `--skip-nidm`: Skip NIDM conversion step
+- `--num-threads`: Number of threads to use for processing (default: 1)
+- `--verbose`: Print detailed logs
+
+## Outputs
+
+The app generates the following outputs:
+
+- Segmentation results in BIDS-compatible format
+- Probability maps for each tissue class
+- Binary masks for each tissue class
+- NIDM-compatible outputs for reproducibility
+
+## NIDM Outputs
+
+The app generates NIDM-compatible outputs that can be used with NIDM tools for visualization and sharing of results. The NIDM outputs include:
+
+- Segmentation statistics
+- Brain volumes
+- Tissue volumes
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.
+
+## Citation
+
+If you use this BIDS App in your research, please cite:
+
+```
+ANTs BIDS App. ReproNim. https://github.com/ReproNim/ants-bidsapp
+```