Here you can find links to implementations of some of my 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

Training convolutional networks for brain MRI analysis with synthetic data

PV-SynthSeg / PVseg: segmenting MRI scans of any contrast and resolution

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.