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app-classifyber

Linear classification of single streamlines.

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.

apss2bids

Convert APSS file data structure to BIDS standard

attend-fmri-scripts

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

bl_app_dbb_disseg

Deep Learning based segmentation for distorted brains

bl_app_dbb_preproc_t1w

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

brin2014

Code of the experiments described in the paper for Brain Informatics 2014.

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.

covid-net

COVID-Net Open Source Initiative

dataset2bids

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

decmeg2014

Official Repository of the code associated with the data analysis competition DecMeg2014

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

hcp-tractography

Dipy pipeline for reconstruction and tracking of tractography from Human Connectome Project dataset

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).

neurobox

A OwnCloud Plugin to manage data analysis on remote high performance computing infrastructure.

prni2016_brain_network_tutorial

Materials of tutorial on Brain Network Analysis at PRNI2016

pykore

The scripts to install a neuroimaging python environment on high performace computing infrastructure.

rtfmridecoding

Setup for real-time brain decoding of functional MRI

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

tractome

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