Freesurfer Python Packages

clinica

Software platform for clinical neuroimaging studies

pydra-freesurfer

Pydra tasks for FreeSurfer designed for Clinica

visualqc

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

subcortexmesh

A python toolbox for automated conversion of subcortical segmentation volumes to surface meshes and computation of vertex-wise metrics

graynet

Subject-wise networks from structural MRI, both vertex- and voxel-wise features (thickness, GM density, curvature, gyrification)

brainload

A python module designed to reduce your brain load while accessing FreeSurfer brain surface and morphometry data files of single subjects and groups.

freesurfer-volume-reader

Python script & library to read hippocampal volumes computed by Freesurfer & ASHS

freesurfer-surface

Python Library to Read and Write Surface Files in Freesurfer's TriangularSurface Format

freesurfer-stats

Python Library to Read FreeSurfer's Cortical Parcellation Anatomical Statistics

dartseg

Code for DARTS: DenseUnet-based Automatic Rapid Tool for brain Segmentation

mri2mne

Complete pipeline from an MRI in DICOM + an EEG recording to a cortical source estimate with MNE-Python. Driven in Python, runs natively on Windows, without FreeSurfer, without WSL, without Docker. (An optional volumetric BEM route is described further down; that one does use WSL + FreeSurfer.)

clinica-pydra-freesurfer

Pydra tasks for FreeSurfer designed for Clinica