NILab Neuroinformatics Laboratory's repositories
HCP-Tractography
Dipy pipeline for reconstruction and tracking of tractography from Human Connectome Project dataset
app-classifyber
Linear classification of single streamlines.
bl_app_dbb_preproc_t1w
Brainlife App for the preprocessing of T1w MRI data of Distorted Brain Benchmark
supervised_causality_detection
Code associated with the paper Classification-based Causality Detection in Brain Recording
tractogram_filtering
Filtering out of artifactual streamlines from a tractogram with a geometric deep learning model
app-classifyber-segmentation
Code to run Classifyber as a pre-trained bundle segmentation method.
APSS-Tractography
Pipeline for processing diffusion MRI and recostruncting deterministic tractography according to the requirement of the Neurosurgery Department of APSS Trentino.
bl_app_dbb_DisSeg
Deep Learning based segmentation for distorted brains
WBIR2020_experiments
Code for the experiments of the manuscript "Nonlinear Alignment of Whole Tractograms with the Linear Assignment Problem" submitted to WBIR2020 (https://wbir2020.org)
benchmark_bundle_segmentation
Code for benchmarking automatic bundle segmentation methods.
bl_app_dbb_ANTsCTSeg
A tool that performs the antsCorticalThickness.sh script on a T1-w image using PTBP priors in order to obtain the brain tissue segmentation.
bl_app_dbb_DiceScore
Tool that performs the dice score between two 3D segmentations
causality_prediction_cortical_model
Classification-based Prediction of Effective Connectivity Between Timeseries with a Realistic Cortical Network Model.
classifyber-seg
Repository for the docker to segment with Classifyber.
Dataset2BIDS
Tool for converting DICOM folders to a standard BIDS format dataset, with extra options for longitudinal pre-/post-surgical MRI data.
eye-movements
Collection of scripts to manage and analyze eye - movements data
fractal_dimension
Investigation on the fractal dimension of segmented white matter bundles.
graph_matching_tractograms
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
intraopmap
Integrating direct brain stimulation with rsfMRI and tractography data
kernel_two_sample_test
A python implementation of the kernel two-samples test as in Gretton et al 2012 (JMLR).
LAP_tract_segmentation
Code for automatic segmentation of tract/bundles from tractography data based on the linear assignment problem (LAP).
prni2016_brain_network_tutorial
Materials of tutorial on Brain Network Analysis at PRNI2016
rtfMRIdecoding
Setup for real-time brain decoding of functional MRI
Tractome_Segmentation
Generation of segmentation session suitable for Tractome toolkit
TractSeg-BrainLife
Automatic White Matter Bundle Segmentation