Here you can find links to implementations of some of our published methods:
Segmentation of brain subregions in FreeSurfer:
Analysis of brain MRI scans of any resolution and contrast:
Brain extraction (skull stripping)
3D histology reconstruction
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.