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@FBK-NILab NILab Neuroinformatics Laboratory

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    35 repositories

    • FBK-NILab.github.io

      Public
      Website of Neuroinformatics Laboratory at Fondazione Bruno Kessler and University of Trento
      SCSS
      •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • 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
      •0•5•0•0•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
      •0•1•1•0•Updated Dec 26, 2023Dec 26, 2023

    • TractSeg-BrainLife

      Public
      Automatic White Matter Bundle Segmentation
      Python
      •
      Apache License 2.0
      •76•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

    • 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 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
      •0•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

    • tractome

      Public
      Tractome is an interactive 3D tool for exploration and segmentation of tractography data.
      Python
      •
      Other
      •5•6•7•2•Updated Sep 23, 2021Sep 23, 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
      •2•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
      •477•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
      •3•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

    • prni2016_brain_network_tutorial

      Public
      Materials of tutorial on Brain Network Analysis at PRNI2016
      0•0•0•0•Updated Jun 17, 2016Jun 17, 2016

    • kernel_two_sample_test

      Public
      A python implementation of the kernel two-samples test as in Gretton et al 2012 (JMLR).
      Python
      •12•0•0•0•Updated Apr 21, 2016Apr 21, 2016