138 Works

FSL Top-up & Eddy

Brad Caron
This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.


This application will copy "lh.hippoSfVolumes-T1.v10.txt" and "rh.hippoSfVolumes-T1.v10.txt" from Freesurfer's parcellation to an output directory.

workbench test

David Hunt

Tissue-type segmentation

Brad Caron & Brent McPherson
This app will generate a 5-tissue type mask (5tt) from a T1 anatomical image using mrtrix3's 5ttgen. This code was adapted from app-mrtrix3-act (https://brainlife.io/app/5aac2437f0b5260027e24ae1), written by Brent McPherson (bcmcpher@iu.edu).

Denoise SOS-reconstructed DWI data

Brad Caron & Sophia Vinci-Booher

Extract b0 images from DWI

Brad Caron & Sophia Vinci-Booher
This app will extract the b0 images from a DWI image using MrTrix3’s dwiextract function. Will output both the b0 and the non b0 images.

Bayesian Analysis of Retinotopic Maps

David Hunt

OHBM 2020: The brainlife.io cloud-services for functional network neuroscience

Conner Victory, David Hunt, Franco Delogu, Franco Pestilli, Josh Faskowitz & Soichi Hayashi
Example of functional connectivity matrices constructed using Brainlife.io.

DSC evaluation (wmc - trk)

Giulia Berto
Compute the Dice Similarity Coefficient (DSC) between corresponding tracts of the given segmentation and the ground truth when using HCP data.

fMRI to Connectivity Matrices - test

Soichi Hayashi & Josh Faskowitz
fmriprep outputs to connectivity matrices



Track between multiple brain regions from atlas (new wmc output)

Franco Pestilli & Daniel Bullock
To track between ROIS from atlas, please run "Generate ROIs from an atlas" App (https://brainlife.io/app/5c364d71836af601cc85864d), then run "ROI to ROI Tracking" App (https://brainlife.io/app/5e516420cb80941d63f51b0e)

Peaks extraction

Giulia Berto
App to extract the peaks of a spherical harmonic function at each voxel.

AnalyzepRF on volume

Brad Caron & David Hunt
An app to do a population receptive field analysis on HCP 7T retinotopy fMRI data


Aditya Gupta
This is an application I am developing for the Franco Pestilli's Brainlife Platform.

White Matter Anatomy Segmentation

Brad Caron, Daniel Bullock, Franco Pestilli, Giulia Berto & Soichi Hayashi
An automated segmentation of major white matter tracts from an input whole brain tractography. Utilizes a WMQL-like approach (https://tract-querier.readthedocs.io/en/latest/) to segment streamlines, as documented in Bullock et al. 2019 (https://doi.org/10.1007/s00429-019-01907-8). Makes extensive use of the wma tools library (https://github.com/DanNBullock/wma_tools).

QSIPrep (under development)

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Preprocessing and reconstruction of diffusion MRI

Track The Human Optic RAdiation (THORA): Contrack - Tracking Eccentricity

Brad Caron

Detect ECG artifacts

Alexandre Gramfort, Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
A sample brainlife app that uses EEG data (fif)

Bin cortical volume and thickness by eccentricity

Brad Caron
This app will bin values of cortical thickness and volume from the Freesurfer pial surface by pRF eccentricity. This app takes as input a Freesurfer segmentation and a pRF mapping and outputs both a .mat structure and graph pngs.

Penumbra Analysis

Brad Caron & Brielle Stark

Track The Human Optic RAdiation (THORA): mrtrix2 - Eccentricity

Brad Caron
This app will perform ensemble tracking between 2 or more cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. The app will automatically generate ROI niftis in diffusion space for tracking based on inputted ROI numbers. Inputs include: parcellation (freesurfer; atlas optional), dt6 from dtiinit, and ROI pairings. Outputs include a track.tck for each pairing of ROIs, a classification structure, and a fg_classified structure which can then be fed into...


Anibal Solon Heinsfeld, Brad Caron, Cameron Craddock, Franco Pestilli, Giulia Berto & Soichi Hayashi
Configurable Pipeline for the Analysis of Connectomes

Connectome Mapper

David Hunt
Generate connection matrix for BIDS directories

Attention ROI warp

Daniel Bullock & Ilaria Sani
This service aligns two sets of Regions of Interest (ROIs) from Sani et al., in preparation to the individual subject space. A first set of ROIs has been obtained by thresholding functional MRI data. A second set of ROIs has been obtained by creating sphere ROIs around the peak of functional MRI activation. The ROIs are stored here: https://github.com/brainlife/VisWMROIWarp/tree/master/rois

Registration Year

  • 2019

Resource Types

  • Software