Installation

BIDS App for Structural Connectivity Applied To Targeted Regions (SCATTR)

Requirements

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

  • For those wishing to contribute or modify the code, pip install or poetry install are also available (Linux), but will still require Singularity to handle some dependencies. See Contributing to SCATTR.

  • Note: Apple ARM-based chips (e.g. M1, M2, etc.) are not currently supported. We do not have a Docker arm64 container yet.

Notes

  • Inputs to SCATTR should be a BIDS dataset, including processed Freesurfer and DWI derivatives (which can be stored separately).

Docker on Windows / Mac (Intel) / Linux

The SCATTR 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