12. Software Used

This Glossary provides brief descriptions of commonly used neuroimaging tools along with links to their official documentation and license information.

AFNI

AFNI is a suite of tools for processing and analyzing fMRI data, including preprocessing, statistical modeling, and interactive visualization. Licensed under the AFNI Public License (similar to BSD, free for academic use).

ANTs

ANTs is a suite for high‑performance image registration, template building, and segmentation, known for state‑of‑the‑art nonlinear registration algorithms. Licensed under the Apache 2.0 license.

CAT12

CAT12 is a structural MRI analysis toolbox within SPM, providing advanced segmentation, surface extraction, and morphometry (VBM, SBM, RBM). Distributed under the CAT12 academic license (free for non‑commercial research).

fMRIPrep

fMRIPrep is a robust and standardized preprocessing pipeline for functional MRI data, integrating best practice tools for motion correction, distortion correction, anatomical alignment, and confound estimation. Licensed under the BSD 3-Clause license.

FreeSurfer

FreeSurfer is a software package for cortical surface reconstruction, segmentation, and surface‑based morphometry. Licensed under the FreeSurfer Software License (free for academic and non‑commercial use).

FSL

FSL is a comprehensive collection of tools for MRI analysis, including registration (FLIRT, FNIRT), segmentation (FAST), and fMRI modeling (FEAT). Licensed under the FSL License (free for non‑commercial use).

MRIQC

MRIQC is a tool for automated extraction of image quality metrics (IQMs) from structural, functional, and diffusion MRI scans. It helps detecting artifacts, outliers, and acquisition issues without manual inspection. Licensed under the BSD 3-Clause license.

Nilearn

Nilearn is a Python library for statistical learning and visualization of neuroimaging data, supporting decoding, connectivity analysis, and interactive plotting. Licensed under the BSD 3-Clause license.

Nipype

Nipype is a Python framework providing a unified interface to major neuroimaging tools (SPM, FSL, AFNI, FreeSurfer, ANTs) and enabling reproducible workflow construction. Licensed under the Apache 2.0 license.

SPM

SPM is a widely used software suite for analyzing brain imaging data sequences, including preprocessing, statistical modeling, and visualization. Licensed under the SPM Academic Software License (free for non‑commercial research).