Installation

Requirements

Docker (Intel Mac/Windows/Linux) or Singularity (Linux)

Notes

Inputs to Labelmerge should be organized as BIDS derivatives, taking one “base” and one “overlay” atlas

Docker on Windows / Mac (Intel) / Linux

The Labelmerge BIDS App is available on DockerHub as versioned releases. Instructions can be found in the Docker documentation page.

Pros

Compatible with non-Linux systems
All dependencies are in a single container

Cons

Typically not possible on shared machines
Cannot use Snakemake cluster execution profiles
Cannot edit code

Singularity Container

The same Docker container can also be used with Singularity (now Apptainer). Instructions can be found in the Singularity / Apptainer documentation page.

Pros

All dependencies are in a single container, stored as a single file (.sif)
Compatible on shared systems with Singularity installed

Cons

Cannot use Snakemake cluster execution profiles
Cannot edit code

Python Environment with Singularity Dependencies

Instructions can be found in the Contributing documentation page.

Pros

Flexibility to modify code

Cons

Only compatible on systems with Singularity for external dependencies

Pip Install

labelmerge can also be installed using pip:

pip install labelmerge

Pros

Ease of installation

Cons

Potential for conflicting dependencies across different packages