Metadata-Version: 2.4
Name: pyfsviz
Version: 0.6.0
Summary: Python tools for FreeSurfer visualization and QA
Author-Email: Lezlie Espana <lespana@mcw.edu>
License-Expression: MIT
License-File: LICENSE
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Documentation
Classifier: Topic :: Software Development
Classifier: Topic :: Utilities
Classifier: Typing :: Typed
Project-URL: Homepage, https://mcw-meier-lab.github.io/pyFSViz
Project-URL: Documentation, https://mcw-meier-lab.github.io/pyFSViz
Project-URL: Changelog, https://mcw-meier-lab.github.io/pyFSViz/changelog
Project-URL: Repository, https://github.com/mcw-meier-lab/pyFSViz
Project-URL: Issues, https://github.com/mcw-meier-lab/pyFSViz/issues
Project-URL: Discussions, https://github.com/mcw-meier-lab/pyFSViz/discussions
Requires-Python: >=3.10
Requires-Dist: fsqc>=2.1.4
Requires-Dist: importlib-resources>=6.5.2
Requires-Dist: matplotlib>=3.10.7
Requires-Dist: nilearn>=0.12.1
Requires-Dist: nipype>=1.10.0
Requires-Dist: nireports>=25.0.1
Requires-Dist: numpy>=2.0.2
Requires-Dist: pandas>=2.3.3
Requires-Dist: plotly>=6.3.1
Description-Content-Type: text/markdown

# pyFSViz

[![ci](https://github.com/mcw-meier-lab/pyFSViz/workflows/ci/badge.svg)](https://github.com/mcw-meier-lab/pyFSViz/actions?query=workflow%3Aci)
[![documentation](https://img.shields.io/badge/docs-mkdocs-708FCC.svg?style=flat)](https://mcw-meier-lab.github.io/pyFSViz/)
[![pypi version](https://img.shields.io/pypi/v/pyfsviz.svg)](https://pypi.org/project/pyfsviz/)

Python tools for FreeSurfer visualization and QA. pyFSViz builds HTML reports
from existing `recon-all` output (individual screenshots and group metric
summaries). It does not run FreeSurfer reconstructions.

> **FreeSurfer and FSL are not part of this install.** Install those tools
> separately and source their setup scripts in the same shell or job before
> using pyFSViz. See
> [Prerequisites](https://mcw-meier-lab.github.io/pyFSViz/user-guide/prerequisites/).

## Installation

Requires Python 3.10 or newer. This installs the Python package only.

```bash
pip install pyfsviz
```

With [`uv`](https://docs.astral.sh/uv/):

```bash
uv tool install pyfsviz
```

## Usage

After [FreeSurfer and FSL are initialized](https://mcw-meier-lab.github.io/pyFSViz/user-guide/prerequisites/):

```python
from pyfsviz import FreeSurfer

fs = FreeSurfer()
fs.gen_batch_reports("reports/")
fs.gen_group_report("reports/")
```

See the [quick start](https://mcw-meier-lab.github.io/pyFSViz/user-guide/quickstart/)
for output layout, group comparisons, and batch flags.
