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.
Installation
Requires Python 3.10 or newer. This installs the Python package only.
pip install pyfsviz
With uv:
uv tool install pyfsviz
Usage
After FreeSurfer and FSL are initialized:
from pyfsviz import FreeSurfer
fs = FreeSurfer()
fs.gen_batch_reports("reports/")
fs.gen_group_report("reports/")
See the quick start for output layout, group comparisons, and batch flags.
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