Installation

AutoAFIDs: A BIDS App for Automatic Landmark Localization

AutoAFIDs is a BIDS App that automatically detects anatomical landmarks in the human brain. It is trained to predict the coordinates of a standardized set of well-validated anatomical landmarks (e.g., the anterior and posterior commissures).

🧰 System Requirements

we support three modes for installing AutoAFIDs:

Method

OS Support

Container Needed

Editable

Cluster Profiles

Notes

Conda

Linux, macOS (Intel & M2 only)

❌ No

βœ… Yes

βœ… Yes

Recommended for most local setups

Docker

Windows, macOS (Intel/Silicon)

βœ… Yes

❌ No

❌ No

Works cross-platform (slow on M1)

Singularity/Apptainer

Linux only

βœ… Yes

❌ No

❌ No

Good for HPC or shared environments

πŸ’‘ Note: GPU is not required.
⚠️ Apple Silicon (M1): Native Conda support is not available. You can use Docker with emulated amd64, but performance will be slow.

If you’re interested in contributing to development, see the Contributing Guide.

πŸ“‚ Inputs and Outputs

  • Input: BIDS-formatted dataset containing structural MRI images (best on T1-weighted modalities).

  • Output: Automatically placed anatomical fiducials (AFIDs) saved as structured coordinate files and visualizations (if using --fidqc flag).

πŸš€ Installation Methods

πŸ”§ 1. Conda Environment (Linux/macOS)

AutoAFIDs can be installed via Conda for container-free execution on Linux and Intel macOS systems.

πŸ“˜ Conda Installtion Instructions

βœ… Pros:

  • Easy to install and run

  • Fully editable code

  • Works with Snakemake profiles

⚠️ Cons:

  • Not supported on Windows or Apple Silicon (M1) system

  • Requires Conda or Miniconda

🐳 2. Docker Container (Windows/Linux/macOS Intel)

A pre-built Docker container is available with all dependencies bundled.

πŸ“˜ Docker Setup Instructions

βœ… Pros:

  • Cross-platform support, including limited M1 compatibility via emulation

  • All dependencies packaged in a single file

⚠️ Cons:

  • Cannot edit code inside the container

  • Not compatible with Snakemake cluster execution

  • May not be usable on shared systems (e.g., university clusters)

πŸ§ͺ 3. Singularity / Apptainer (Linux)

Use Singularity (now Apptainer) to convert the Docker image into a .sif file for HPC or institutional clusters.

πŸ“˜ Singularity Setup Instructions

βœ… Pros:

  • Ideal for shared Linux systems

  • All dependencies packaged in a single file

⚠️ Cons:

  • Cannot edit code inside the container

  • Not compatible with Snakemake cluster execution