Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: tractography
carpentries-incubator/SDC-BIDS-dMRI
Introduction to dMRI
Language: Jupyter Notebook - Size: 41 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 20 - Forks: 16
mfroeling/QMRITools
Processing and visualization tools for quantitative MRI data
Language: Mathematica - Size: 537 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 57 - Forks: 17
tractor/tractor
Magnetic resonance imaging and tractography with R
Language: C++ - Size: 106 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 28 - Forks: 8
DelinteNicolas/UTracto
Package facilitating the tracking of sub-cortical U-Fibers
Language: Python - Size: 36.4 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 3 - Forks: 0
dipy/dipy
DIPY is the paragon 3D/4D+ 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: 70.2 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 669 - Forks: 428
MIC-DKFZ/MITK-Diffusion
MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit
Language: C++ - Size: 15.8 MB - Last synced: 5 days ago - Pushed: about 2 months ago - Stars: 69 - Forks: 15
DelinteNicolas/UNRAVEL
This repository contains the code of UtiliziNg tRActography to uncoVEr muLti-fixel microstructure (UNRAVEL).
Language: Python - Size: 46.4 MB - Last synced: 3 days ago - Pushed: 23 days ago - Stars: 6 - Forks: 1
PennLINC/qsiprep
Preprocessing and reconstruction of diffusion MRI
Language: HTML - Size: 178 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 129 - Forks: 52
SlicerDMRI/SlicerWMA-OLD
Extension for 3D slicer that provides a module and a python package for fiber clustering and tractography analysis.
Language: Python - Size: 98.6 KB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 0 - Forks: 3
raamana/neuropredict
Easy and comprehensive assessment of predictive power, with support for neuroimaging features
Language: Python - Size: 16.4 MB - Last synced: 5 days ago - Pushed: about 2 months ago - Stars: 100 - Forks: 26
lorifranke/FiberStars
Source code for FiberStars, a visualization tool for comparing dMRI data of multiple subjects.
Language: JavaScript - Size: 94 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 5 - Forks: 1
Slicer/Slicer
Multi-platform, free open source software for visualization and image computing.
Language: C++ - Size: 121 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1,459 - Forks: 502
ruizengalways/FOD-Net
FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution
Language: Python - Size: 7.18 MB - Last synced: 12 days ago - Pushed: about 2 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: about 1 month ago - Pushed: 3 months ago - Stars: 9 - Forks: 1
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 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 19 - Forks: 6
dPys/PyNets
A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning
Language: Python - Size: 1010 MB - Last synced: 29 days ago - Pushed: 4 months ago - Stars: 117 - Forks: 41
scil-vital/TrackToLearn
Public release of Track-to-Learn: A general framework for tractography with deep reinforcement learning
Language: Python - Size: 78.5 MB - Last synced: 5 days ago - Pushed: 15 days ago - Stars: 14 - Forks: 10
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: about 2 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0
SlicerDMRI/slicerdmri.github.io
SlicerDMRI organization website repository
Language: JavaScript - Size: 427 MB - Last synced: about 2 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 3
brainlife/app-track-between-multiple-regions
Language: Shell - Size: 131 MB - Last synced: about 2 months ago - Pushed: about 4 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: about 2 months ago - Pushed: about 4 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: about 2 months ago - Pushed: 7 months ago - Stars: 4 - Forks: 9
SlicerDMRI/whitematteranalysis
White matter tractography clustering and more...
Language: Python - Size: 203 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 60 - Forks: 30
SlicerDMRI/SlicerDMRI
Diffusion MRI analysis and visualization in 3D Slicer open source medical imaging platform.
Language: C++ - Size: 6.1 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 71 - Forks: 27
SlicerDMRI/ORG-Atlases
ORG Fiber Clustering White Matter Atlas
Size: 1.46 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 23 - Forks: 6
Slicer/SlicerGitSVNArchive
:warning: OBSOLETE | Multi-platform, free open source software for visualization and image computing.
Language: C++ - Size: 448 MB - Last synced: 3 months ago - Pushed: about 2 years ago - Stars: 875 - Forks: 468
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: 3 months ago - Pushed: 3 months 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: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
clintg6/DSN
Python tool for spatially normalizing diffusion MRI data
Language: Python - Size: 10.7 KB - Last synced: 4 months ago - Pushed: over 5 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: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0
cwatson/brainGraph
Graph theory analysis of brain MRI data
Language: R - Size: 5.65 MB - Last synced: 4 months ago - Pushed: about 3 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: 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
scil-vital/tractolearn
Tractography learning
Language: Python - Size: 576 KB - Last synced: 5 days ago - Pushed: 6 months 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: 5 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 4
SlicerDMRI/wmap
White Matter Analysis Pipeline (WMAP)
Language: Python - Size: 78.1 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
TylerSpears/fenri
FENRI (Fiber Orientations from Explicit Neural Representations) Implementation Repository
Language: Jupyter Notebook - Size: 43 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
delucaal/MRIToolkit
Language: MATLAB - Size: 8.33 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 22 - Forks: 5
vindasna/GeoLab
Geolab : Geometric-based tractography parcellation of Superficial white matter
Language: C++ - Size: 2.61 GB - Last synced: 6 months ago - Pushed: 6 months 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: 4 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 2
esinkarahan/ATA
Along Tract Analysis of Diffusion Weighted Images
Language: MATLAB - Size: 4.18 MB - Last synced: 6 months ago - Pushed: almost 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: 7 months ago - Pushed: 7 months 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: about 2 months ago - Pushed: 4 months 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: 7 months ago - Pushed: over 5 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: 7 months ago - Pushed: over 3 years ago - Stars: 8 - Forks: 5
cwatson/mri_library
Scripts for MRI preprocessing
Language: Shell - Size: 146 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 8 - Forks: 3
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: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
MASILab/STrUDeL
Streamline Tractography Utilities for Deep Learning
Language: Python - Size: 38.3 MB - Last synced: about 1 month ago - Pushed: 12 months 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: 10 months ago - Pushed: over 3 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: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
rmukh/ukftractography Fork of pnlbwh/ukftractography
Unscented Kalman filter for brain tractography
Language: C - Size: 204 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
djoerch/randomised_filtering
Code for randomised tractogram filtering using rSIFT
Language: Python - Size: 120 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0
DelinteNicolas/TractAnalysis
Analysis of the structural connectivity of diffusion data
Language: Python - Size: 7.42 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0
brain-life/encode
Method for encoding brain connectomes in multidimensional arrays (tensors).
Language: MATLAB - Size: 2.61 MB - Last synced: 3 months ago - Pushed: about 3 years ago - Stars: 39 - Forks: 25
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: about 8 hours ago - Pushed: over 1 year ago - Stars: 5 - Forks: 2
jasonbian97/fastcod-code
A fast python tool for extracting diffusion-based brain connectivity
Language: Python - Size: 589 KB - Last synced: 7 months ago - Pushed: 7 months 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: 7 months ago - Pushed: 7 months 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: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
benoit-dubreuil/inm5803-ete2022 📦
White matter fiber tracts configuration generator
Language: TeX - Size: 11.7 MB - Last synced: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
jasonbian97/fastconn
A tool for extracting diffusion-based brain connectivity
Language: Python - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
Apsis/TrainTracts
Blender plugin for rendering brain tractography (.tck) files!
Language: Python - Size: 19.1 MB - Last synced: about 1 year ago - Pushed: almost 2 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: about 1 year ago - Pushed: almost 3 years ago - Stars: 6 - Forks: 4
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: about 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 6
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: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0
chamberm/fibernavigator Fork of scilus/fibernavigator
FiberNavigator - Maxime Chamberland -
Language: C++ - Size: 10.5 MB - Last synced: 12 months ago - Pushed: over 2 years ago - Stars: 10 - Forks: 2
bdezonia/trconv
Tractography file converter
Language: Java - Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
banctilrobitaille/BrainGym
A toolkit for developing reinforcement algorithm for diffusion weighted image analysis.
Size: 1.95 KB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0
axiezai/pipetography
Nipype and tractography!
Language: Jupyter Notebook - Size: 64.2 MB - Last synced: 23 days ago - Pushed: almost 2 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: about 1 year ago - Pushed: over 2 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: about 1 year ago - Pushed: over 2 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: 12 months ago - Pushed: almost 3 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: about 1 year ago - Pushed: about 3 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: about 1 year ago - Pushed: over 3 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: about 1 year ago - Pushed: over 3 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: about 1 year ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0
NIRALUser/AutoTract Fork of jeanyves-yang/AutoTract
Automatic Tractography Tool
Language: CMake - Size: 7.78 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 4
brainlife/ui-fibernavigator
Docker container for FiberNavigator for Brainlife.io
Language: Shell - Size: 1.47 MB - Last synced: about 1 month ago - Pushed: over 5 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: about 1 month ago - Pushed: 12 months 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: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0
chrisfoulon/Parcellotron
Connectivity-based parcellation
Language: Python - Size: 120 KB - Last synced: 10 months ago - Pushed: about 5 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: 27 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1