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)
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.