Repositories list

• tractome

  Public
  Tractome is an interactive 3D tool for exploration and segmentation of tractography data.

  Python

  •

  Other

  •6•7•7•2•Updated Jul 31, 2025Jul 31, 2025

• White-Matter-DES-Brain-Maps

  Public
  White matter brain maps derived from DES and MRI, both rsfMRI and DWI.

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

• FBK-NILab.github.io

  Public
  Website of Neuroinformatics Laboratory at Fondazione Bruno Kessler and University of Trento

  SCSS

  •0•0•0•0•Updated Jun 22, 2025Jun 22, 2025

• Warp_V-Norm

  Public
  Python

  •1•0•0•0•Updated May 26, 2025May 26, 2025

• bl_app_dbb_preproc_t1w

  Public
  Brainlife App for the preprocessing of T1w MRI data of Distorted Brain Benchmark

  Shell

  •1•2•0•0•Updated May 21, 2025May 21, 2025

• bl_app_dbb_DisSeg

  Public
  Deep Learning based segmentation for distorted brains

  Python

  •1•1•0•0•Updated Jun 18, 2024Jun 18, 2024

• verifyber

  Public
  An extended edge convolution model for tractography

  Python

  •3•6•0•1•Updated Apr 30, 2024Apr 30, 2024

• intraopmap

  Public
  Integrating direct brain stimulation with rsfMRI and tractography data

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 28, 2023Dec 28, 2023

• app-classifyber-segmentation

  Public
  Code to run Classifyber as a pre-trained bundle segmentation method.

  segmentationwhite-matter-segmentation

  Python

  •

  MIT License

  •1•1•1•0•Updated Dec 26, 2023Dec 26, 2023

• TractSeg-BrainLife

  Public
  Automatic White Matter Bundle Segmentation

  Python

  •

  Apache License 2.0

  •75•0•0•0•Updated Nov 6, 2023Nov 6, 2023

• tractogram_filtering

  Public
  Filtering out of artifactual streamlines from a tractogram with a geometric deep learning model

  Jupyter Notebook

  •1•2•2•0•Updated May 3, 2023May 3, 2023

• Dataset2BIDS

  Public
  Tool for converting DICOM folders to a standard BIDS format dataset, with extra options for longitudinal pre-/post-surgical MRI data.

  Shell

  •0•0•0•0•Updated Jan 17, 2023Jan 17, 2023

• bl_app_dbb_DiceScore

  Public
  Tool that performs the dice score between two 3D segmentations

  Python

  •1•0•0•0•Updated Jul 17, 2022Jul 17, 2022

• bl_app_dbb_ANTsCTSeg

  Public
  A tool that performs the antsCorticalThickness.sh script on a T1-w image using PTBP priors in order to obtain the brain tissue segmentation.

  Shell

  •1•0•0•0•Updated Jul 17, 2022Jul 17, 2022

• WBIR2020_experiments

  Public
  Code for the experiments of the manuscript "Nonlinear Alignment of Whole Tractograms with the Linear Assignment Problem" submitted to WBIR2020 (https://wbir2020.org)

  Python

  •1•1•0•0•Updated Mar 1, 2022Mar 1, 2022

• benchmark_bundle_segmentation

  Public
  Code for benchmarking automatic bundle segmentation methods.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 22, 2021Dec 22, 2021

• classifyber-seg

  Public
  Repository for the docker to segment with Classifyber.

  Python

  •0•0•0•0•Updated Jan 14, 2021Jan 14, 2021

• app-classifyber

  Public
  Linear classification of single streamlines.

  Python

  •

  MIT License

  •3•7•0•0•Updated Jan 12, 2021Jan 12, 2021

• fractal_dimension

  Public
  Investigation on the fractal dimension of segmented white matter bundles.

  Python

  •1•0•0•0•Updated Oct 15, 2020Oct 15, 2020

• COVID-Net

  Public
  COVID-Net Open Source Initiative

  Python

  •

  Other

  •478•0•0•0•Updated Jul 8, 2020Jul 8, 2020

• Tractome_Segmentation

  Public
  Generation of segmentation session suitable for Tractome toolkit

  Python

  •0•0•0•0•Updated Oct 10, 2019Oct 10, 2019

• apss2bids

  Public
  Convert APSS file data structure to BIDS standard

  Shell

  •0•0•0•0•Updated Oct 8, 2019Oct 8, 2019

• APSS-Tractography

  Public
  Pipeline for processing diffusion MRI and recostruncting deterministic tractography according to the requirement of the Neurosurgery Department of APSS Trentino.

  Python

  •

  GNU Lesser General Public License v3.0

  •5•1•0•0•Updated Jul 22, 2019Jul 22, 2019

• LAP_tract_segmentation

  Public
  Code for automatic segmentation of tract/bundles from tractography data based on the linear assignment problem (LAP).

  Python

  •

  MIT License

  •4•0•0•0•Updated Jul 16, 2018Jul 16, 2018

• causality_prediction_cortical_model

  Public
  Classification-based Prediction of Effective Connectivity Between Timeseries with a Realistic Cortical Network Model.

  C

  •1•0•0•0•Updated Apr 20, 2018Apr 20, 2018

• graph_matching_tractograms

  Public
  This is the code of the algorithm described in: Olivetti E, Sharmin N and Avesani P (2016) Alignment of Tractograms As Graph Matching. Front. Neurosci. 10:554. doi: 10.3389/fnins.2016.00554

  Python

  •2•0•0•0•Updated Dec 14, 2017Dec 14, 2017

• rtfMRIdecoding

  Public
  Setup for real-time brain decoding of functional MRI

  MATLAB

  •

  BSD 2-Clause "Simplified" License

  •2•0•0•0•Updated Jul 14, 2017Jul 14, 2017

• attend-fmri-scripts

  Public
  Python

  •1•0•0•0•Updated Sep 12, 2016Sep 12, 2016

• eye-movements

  Public
  Collection of scripts to manage and analyze eye - movements data

  Python

  •1•0•0•0•Updated Sep 9, 2016Sep 9, 2016

• supervised_causality_detection

  Public
  Code associated with the paper Classification-based Causality Detection in Brain Recording

  Python

  •

  MIT License

  •3•2•0•0•Updated Aug 3, 2016Aug 3, 2016