Here you can find links to implementations of some of our published methods:


Segmentation of brain subregions in FreeSurfer:

Hippocampal subfields and nuclei of the amygdala (cross sectional and longitudinal)

Thalamic nuclei

Brainstem substructures

Subregions of the hypothalamus


Analysis of brain MRI scans of any resolution and contrast:

SynthSeg: segmenting MRI scans of any contrast and resolution without retraining,

SynthSR: joint super-resolution and synthesis to generate 1 mm MPRAGE volumes from clinical scans.


Brain extraction (skull stripping)

ROBEX: robust brain extraction


3D histology reconstruction

Refinement of nonlinear registrations in histology reconstruction

A multimodal computational pipeline for 3D histology of the human brain


Other software:

BIAS FIELD & SLAB BOUNDARY ARTIFACT CORRECTION: simultaneous correction of bias field and slab boundary artifacts in multi-slab MRI scans.

MOTION ESTIMATION: Caffe model files for 3D U-net  that estimates whether individual voxels are corrupted by motion artifacts or not.