Name: Jon Haitz Legarreta Gorroño
Type: User
Company: Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School
Bio: Postdoctoral research fellow interested in diffusion MRI, tractography, deep learning, computational neuroanatomy and reproducible scientific research
Location: Boston, MA, USA
Blog: https://jhlegarreta.github.io/
Jon Haitz Legarreta Gorroño's Projects
Microstructure Diffusion Toolbox
mesh geometry tools
MetaImage is the text-based tagged file format for medical images that resulted. We have now extended that file format to support a variety of objects that occur in medicine such a tubes (for vessels, needles, etc.), blobs (for arbitrary shaped objects), cubes, spheres, etc. The complete library is known at MetaIO.
A Spline-Driven Image Slicer
Automated anatomical brain label/shape analysis software (+ website)
:triangular_ruler: A flexible two-column Jekyll theme. Perfect for personal sites, blogs, and portfolios hosted on GitHub or your own server.
missing data handing: visualize and impute
A Python library for Analytic Tractography
Machine Learning Experiment Manager for HPC (SLURM and Moab)
DLTK Model Zoo
Deface Detector for MRI images.
MRtrix provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
ITK remote module from an IJ article at http://www.insight-journal.org/browse/publication/915
NeuroData's MRI Graphs (ndmg) - structural connectome estimation package and pipeline
Torch implementation of neural style algorithm
WebGL-based viewer for volumetric data
A DSL for data-driven computational pipelines
Python package to access a cacophony of neuro-imaging file formats
An open-source convolutional neural networks platform for research in medical image analysis and image-guided therapy
Tools to automatise simple manipulations and measurements of medical images and segmentations in nifti format.
Machine learning for NeuroImaging in Python
Neuroimaging in Python FMRI analysis package
Main website for the Neuroimaging in Python community
Workflows and interfaces for neuroimaging packages
This tool normalizes Diffusion Weighted Images (DWI) gradients.
MIDL 2018: one binary extremely large and inflecting sparse kernel (pytorch)
Code for the PNAS submission
Materials used at the Open Source Software Practices course taught at Rensselaer Polytechnic and at SUNY Albany
Slides for a Talk on Open Source Practices