Installation

License and third-party software

This repository contains a wrapper around CAT12 for research workflows.
CAT12 / SPM12 / MATLAB Runtime (MCR) and other third-party tools are downloaded by the installer and are governed by their respective licenses.
This repository does not distribute CAT12/SPM/MCR binaries.
This project is not affiliated with or endorsed by the CAT12 or SPM developers, nor by The MathWorks.

See THIRD_PARTY_NOTICES.md in the repository root for details.

System requirements

Linux recommended (Ubuntu server works well)
CPU: modern x86_64
RAM: 8GB minimum, 16GB+ recommended (longitudinal + TFCE can be memory heavy)
Disk: enough for the BIDS dataset + derivatives + stats outputs
Tools: bash, wget, unzip, curl, timeout
Python: 3.9+ recommended

What gets installed (workspace-local)

The installer is designed to keep everything inside this repository:

external/cat12/: CAT12 standalone + SPM12
external/MCR/: MATLAB Runtime for CAT12 standalone
external/deno/: Deno runtime (used by bids-validator)
.venv/: Python virtual environment
.env: environment variables consumed by wrappers

Apple Silicon (ARM64) Setup

On macOS with Apple Silicon (M-series chips), native MATLAB requires ARM64 MEX files (.mexmaca64). The standard SPM12 distribution often lacks these.

If using a local MATLAB installation on ARM64:

Ensure your SPM12 installation contains .mexmaca64 binary files. You may need to download a patched/developer version of SPM (e.g., spm25) or compile them manually.
Update config/config.ini to point to the ARM64-compatible SPM path:
```
[SPM]
path = /path/to/arm64_spm
```

Install

From the repo root:

Option A: Standalone (No MATLAB license required)

./scripts/install_cat12_standalone.sh

Option B: Existing MATLAB (Uses your local MATLAB installation)

./scripts/install_cat12_matlab.sh

That’s it. The wrappers (./cat12_prepro, ./cat12_stats) will automatically activate .venv and source .env.

Alternative: Makefile

make install         # For standalone
make install-matlab  # For existing MATLAB
make test

Activate (optional)

You only need this if you want to run Python modules directly:

source activate_cat12.sh

Notes on reproducibility

Python dependencies are installed into .venv.
CAT12 + MCR are installed into external/.
No global installs are required.

Common installation issues

Missing wget / unzip / curl: install via your system package manager.
Corporate proxy / offline: pre-download the CAT12 + MCR zips and adjust the installer URLs or place files into external/ before running.