Slicer/Slicer

Multi-platform, free open source software for visualization and image computing.

Language: C++ - Size: 122 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1,917 - Forks: 598

dPys/PyNets

A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

Language: Python - Size: 1010 MB - Last synced at: 1 day ago - Pushed at: about 1 year ago - Stars: 122 - Forks: 41

mfroeling/QMRITools

Processing and visualization tools for quantitative MRI data

Language: Mathematica - Size: 584 MB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 66 - Forks: 17

tractor/tractor

Magnetic resonance imaging and tractography with R

Language: C++ - Size: 106 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 28 - Forks: 8

dipy/dipy

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

Language: Python - Size: 72.5 MB - Last synced at: 6 days ago - Pushed at: 11 days ago - Stars: 755 - Forks: 446

LaSEEB/structural-connectivity

Code to create structural connectivity matrix from preprocessed DWI and structural MRI data.

Language: Shell - Size: 19.5 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

DelinteNicolas/UNRAVEL

This repository contains the code of UtiliziNg tRActography to uncoVEr muLti-fixel microstructure (UNRAVEL).

Language: Python - Size: 46.9 MB - Last synced at: about 18 hours ago - Pushed at: about 1 month ago - Stars: 22 - Forks: 1

SlicerDMRI/whitematteranalysis

White matter tractography clustering and more...

Language: Python - Size: 203 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 72 - Forks: 34

scil-vital/TrackToLearn

Public release of Track-to-Learn: A general framework for tractography with deep reinforcement learning

Language: Python - Size: 61.3 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 21 - Forks: 10

raamana/neuropredict

Easy and comprehensive assessment of predictive power, with support for neuroimaging features

Language: Python - Size: 16.4 MB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 102 - Forks: 27

carpentries-incubator/SDC-BIDS-dMRI

Introduction to dMRI

Language: Jupyter Notebook - Size: 44.9 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 25 - Forks: 19

SlicerDMRI/wmap

White Matter Analysis Pipeline (WMAP)

Language: Python - Size: 137 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

muscbridge/PyDesigner

A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3k

Language: Python - Size: 47.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 28 - Forks: 7

SlicerDMRI/slicerdmri.github.io

SlicerDMRI organization website repository

Language: TeX - Size: 427 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 3

DanNBullock/WiMSE

A collection of jupyter notebooks designed to provide a comprehensive exploration of concepts related to white matter segmentation.

Language: Jupyter Notebook - Size: 325 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 6

SlicerDMRI/SlicerDMRI

Diffusion MRI analysis and visualization in 3D Slicer open source medical imaging platform.

Language: C++ - Size: 8.37 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 78 - Forks: 27

cwatson/mri_library

Scripts for MRI preprocessing

Language: Shell - Size: 146 KB - Last synced at: 1 day ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 2

delucaal/MRIToolkit

Language: MATLAB - Size: 8.46 MB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 25 - Forks: 4

anamatoso/connectivity-analysis-diffusion

This repository holds the code used in the paper: "Involvement of the cerebellum in structural connectivity enhancement in episodic migraine"

Language: MATLAB - Size: 97.7 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

DelinteNicolas/AUD_microstructure

A repository for the creation of figures and plots for an AUD population study.

Language: Python - Size: 5.45 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

Slicer/SlicerGitSVNArchive

:warning: OBSOLETE | Multi-platform, free open source software for visualization and image computing.

Language: C++ - Size: 448 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 872 - Forks: 458

MIC-DKFZ/MITK-Diffusion

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit

Language: C++ - Size: 15.9 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 76 - Forks: 15

TylerSpears/fenri

FENRI (Fiber Orientations from Explicit Neural Representations) Implementation Repository, presented at the ISBI 2024 conference

Language: Jupyter Notebook - Size: 43 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

matteomancini/trampolino

TRAMPOLINO (TRActography Meta-Pipeline cOmmand LINe tOol) is a CLI for brain tractography. It leverages Nipype to offer an immediate way to reconstruct an orientation distribution function, use it to track the streamlines and eventually filter them, all using existing software toolboxes.

Language: Python - Size: 110 KB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 2

SlicerDMRI/SlicerWMA

Extension for 3D slicer that provides a module and a python package for fiber clustering and tractography analysis.

Language: Python - Size: 104 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 3

brain-life/encode

Method for encoding brain connectomes in multidimensional arrays (tensors).

Language: MATLAB - Size: 2.61 MB - Last synced at: 2 days ago - Pushed at: about 4 years ago - Stars: 38 - Forks: 25

DelinteNicolas/UTracto

Package facilitating the tracking of sub-cortical U-Fibers

Language: Python - Size: 36.4 MB - Last synced at: 9 months ago - Pushed at: 12 months ago - Stars: 3 - Forks: 0

lorifranke/FiberStars

Source code for FiberStars, a visualization tool for comparing dMRI data of multiple subjects.

Language: JavaScript - Size: 94 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1

ruizengalways/FOD-Net

FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution

Language: Python - Size: 7.18 MB - Last synced at: 9 months ago - Pushed at: about 3 years ago - Stars: 17 - Forks: 5

MASILab/cornn_tractography

Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context

Language: Python - Size: 116 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 1

christiennedamatac/tracula

Scripts related to "White Matter Microstructure in Attention-Deficit/Hyperactivity Disorder: A Systematic Tractography Study in 654 Individuals"

Language: Shell - Size: 12.7 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

brainlife/app-track-between-multiple-regions

Language: Shell - Size: 131 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 2

brainlife/app-segment-tracts-between-multiple-regions

Tract Segmentation from input tractography using ROIs

Language: Shell - Size: 55.3 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

brainlife/app-mrtrix3-act

Runs mrtrix3 ACT (Anatomically Constrained Tractography) using either single- or multi-shell diffusion-weighted MRI data.

Language: Shell - Size: 114 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 9

SlicerDMRI/ORG-Atlases

ORG Fiber Clustering White Matter Atlas

Size: 1.46 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 6

LPNC-LANG/MiddleAge_LARA2024

Repo for the article "Dynamics of White Matter Architecture in Lexical Production among Middle-Aged Adults"

Language: MATLAB - Size: 9.03 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

stefanomoriconi/PolarimetricTensorImaging

Generate Polarimetric Tensor Imaging (PTI) together with an Embedded DEMO for Visualisation and Interaction in 3D Slicer.

Size: 16.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

clintg6/DSN

Python tool for spatially normalizing diffusion MRI data

Language: Python - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 3

anamatoso/structural-connectivity-migraine

Detection of structural alterations in episodic migraine using a graph theory approach. This project was done in the scope of my Master's Thesis in Biomedical Engineering.

Language: MATLAB - Size: 3.42 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

cwatson/brainGraph

Graph theory analysis of brain MRI data

Language: R - Size: 5.65 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 159 - Forks: 46

baranaydogan/TrackerYoga

Bend, twist, spread... TrackerYoga is a set of synthetic diffusion MRI data for testing tractography algorithms.

Size: 35.5 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

scil-vital/tractolearn

Tractography learning

Language: Python - Size: 576 KB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 4

KUL-Radneuron/KUL_FWT

Automated tractography using MRTrix3 CSD based on subject-specific parcellations from FreeSurfer and MultiScaleBrainParcellator

Language: Shell - Size: 366 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 4

vindasna/GeoLab

Geolab : Geometric-based tractography parcellation of Superficial white matter

Language: C++ - Size: 2.61 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

alexpron/mrproc

Magnetic Resonance Imaging data processing pipelines with a strong emphasis on the diffusion weighted MRI (DWI) modality and tractogram estimation

Language: Python - Size: 1.29 MB - Last synced at: 6 months ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 2

esinkarahan/ATA

Along Tract Analysis of Diffusion Weighted Images

Language: MATLAB - Size: 4.18 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

Xinyu-Nie/SurfTracker

A novel probabilistic tractography in Superficial White Matter

Language: C - Size: 1.51 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

brainlife/app-mrtrix3-preproc

Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.

Language: Shell - Size: 3.7 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 6

pykao/BraTS2018-survival-prediction

We provide a method to extract the tractographic features from structural MR images for patients with brain tumor

Language: Python - Size: 67.4 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 9 - Forks: 1

3Tissue/MRtrix3Tissue Fork of MRtrix3/mrtrix3

MRtrix3Tissue adds capabilities for 3-Tissue CSD modelling and analysis to a complete version of MRtrix3.

Language: C++ - Size: 24.3 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 5

micerr/Epilepsy-dMRI-VNS

Assessing microstructural brain differences in epileptic patients with vagus nerve stimulation via diffusion MRI, tractography and machine learning

Language: Jupyter Notebook - Size: 270 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

MASILab/STrUDeL

Streamline Tractography Utilities for Deep Learning

Language: Python - Size: 38.3 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

kesshijordan/Kesh_Autoseg_Tools

This is a set of tools associated with automatically segmenting tractography datasets using a combination of two complementary approaches: streamlines included in a fascicle model are identified based on 1) anatomical connectivity priors based on Freesurfer-derived regions of interest (ROIs) in the subject’s native space and 2) shape priors based on 3D streamline bundle atlases applied using Recobundles. The code for a methodology generating bundle atlases is also included, as well as useful command-line helper scripts such as identification of outliers, filtering, and merging functions.

Language: Jupyter Notebook - Size: 1.63 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

rmukh/ukftractography_dp

Diffusion propagator mode for Unscented Kalman Filter brain tractography

Language: C - Size: 204 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

rmukh/ukftractography Fork of pnlbwh/ukftractography

Unscented Kalman filter for brain tractography

Language: C - Size: 204 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

DelinteNicolas/TractAnalysis

Analysis of the structural connectivity of diffusion data

Language: Python - Size: 7.42 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

jasonbian97/fastcod-code

A fast python tool for extracting diffusion-based brain connectivity

Language: Python - Size: 589 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

jasonbian97/fastcod

A fast and valid tool for extracting diffusion-based brain connectivity

Language: HTML - Size: 7.62 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

linum-uqam/inm5803-ete2022-benoit-dubreuil 📦

INM5803 – 3rd COOP internship, B.Sc.A. in Computer Science and Software Engineering

Language: TeX - Size: 11.6 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

benoit-dubreuil/inm5803-ete2022 📦

White matter fiber tracts configuration generator

Language: TeX - Size: 11.7 MB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

linum-uqam/inf6200-h2022-benoit-dubreuil 📦

INF6200 – introduction to research course, B.Sc.A. in Computer Science and Software Engineering

Language: TeX - Size: 812 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

benoit-dubreuil/inf6200-h2022 📦

INF6200 – introduction to research course, B.Sc.A. in Computer Science and Software Engineering

Language: TeX - Size: 813 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

jasonbian97/fastconn

A tool for extracting diffusion-based brain connectivity

Language: Python - Size: 4.88 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Apsis/TrainTracts

Blender plugin for rendering brain tractography (.tck) files!

Language: Python - Size: 19.1 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

NIRALUser/CIVILITY

Cloud Based Interactive Visualization of Tractography Brain Connectome (CIVILITY) is an interactive visualization tool of brain connectome in the web.

Language: JavaScript - Size: 35.5 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 4

djoerch/randomised_filtering

Code for randomised tractogram filtering using rSIFT

Language: Python - Size: 120 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

pykao/ISLES2017-mRS-prediction

This repository extracts the tractograpic feature, other first-order features and the state-of-the-art feature from the stroke lesion. A random forest regressor is used with one type of feature to predict the modified Rankin Scale of stroke patients.

Language: Python - Size: 96.7 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

chamberm/fibernavigator Fork of scilus/fibernavigator

FiberNavigator - Maxime Chamberland -

Language: C++ - Size: 10.5 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 2

bdezonia/trconv

Tractography file converter

Language: Java - Size: 14.6 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

banctilrobitaille/BrainGym

A toolkit for developing reinforcement algorithm for diffusion weighted image analysis.

Size: 1.95 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

axiezai/pipetography

Nipype and tractography!

Language: Jupyter Notebook - Size: 64.2 MB - Last synced at: 22 days ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 2

drombas/streamlines-gsoc

Experiments related with streamlines carried out as part of GSoC 2021.

Language: Jupyter Notebook - Size: 12.9 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

DanNBullock/EcogAnalysisCode

White matter overlap with EEG sites analysis code for Babo-Rebelo et al. 2021

Language: MATLAB - Size: 37.1 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

chamberm/Lesionometry

Tractometry-based metrics for characterizing white matter lesions within fibre pathways

Language: Python - Size: 1010 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1

ayyu/sholl-analysis-matlab

Quick and dirty way of performing Sholl analysis after tractography

Language: MATLAB - Size: 13.7 KB - Last synced at: 2 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

dipy/bl_apps_dipy_track_pft

Brainlife wrapper app for dipy_track_pft workflows.

Language: Shell - Size: 8.79 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

dipy/bl_apps_dipy_track

Brainlife wrapper app for dipy_track workflows.

Language: Shell - Size: 14.6 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

brainhack-ch/tms-tracto

OG 2019 - Project 04: Novel neuronavigation to guide brain stimulation

Language: Jupyter Notebook - Size: 153 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

NIRALUser/AutoTract Fork of jeanyves-yang/AutoTract

Automatic Tractography Tool

Language: CMake - Size: 7.78 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 4

brainlife/ui-fibernavigator

Docker container for FiberNavigator for Brainlife.io

Language: Shell - Size: 1.47 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

brainlife/app-trekker-roi-tracking

Brainlife App (wrapper) for dMRI based fiber tracking between ROIs using parallel transport tractography

Language: Shell - Size: 350 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

karanaggarwal1994/life-gpu-opt

LiFE-GPU-opt software is an optimized implementation of the compute-intensive matrix operations of the LiFE algorithm for GPUs.

Language: MATLAB - Size: 129 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

chrisfoulon/Parcellotron

Connectivity-based parcellation

Language: Python - Size: 120 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1

adliska/autism_connectivity_phd

Source files for my PhD thesis "Brain functional connectivity and its aberrations in mouse models of autism"

Language: TeX - Size: 57.1 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1