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afq

Automated Fiber Quantification

ants

Advanced Normalization Tools (ANTs)

braincovarianceconnecttoolkitv2.1

BCCTv2.1

bru2nii

Bruker ParaVision to NIfTI conversion

bruker2nifti

Medical image format converter: from raw Bruker ParaVision to nifti.

brukergui

Library and GUI for the Bruker data processing

brukermri

Python module to handle Bruker Paravision MRI files (parameter files, raw data, processed data).

cubic_nprot

Code for the image processing and analysis described our Nature Protocols paper.

deep_mri_brain_extraction

3D convolutional neural network for MRI brain extraction

dicomifier

Convert data from Bruker to DICOM and from DICOM to NIfTI

mousebrainatlas

A system for building mouse brain atlas from histology series and automated alignment to atlas

mousemorph

Tools for MRI mouse brain morphometry

niftynet

An open-source convolutional neural networks platform for research in medical image analysis and image-guided therapy

niftyreg_loop_bash

Running NiftyReg in for-loop in MacOS/Unix environment using BASH script.

niftyreg_loop_bat

Running NiftyReg in for-loop using Batch in Windows environment. I highly discourage to install NiftyReg in Windows. Apparently the installation requires Framework 4.0 and older version of Visual Studio (2010?). But the current Windows system (as of May 2016 Framework 4.5) does not support the old library and keeps on rewriting to newer Framework.

niftyseg

seaborn

Statistical data visualization in Python

seaborn-data

Data repository for seaborn examples