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.

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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).

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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.

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Example of functional connectivity matrices constructed using Brainlife.io.

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

fmriprep outputs to connectivity matrices

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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)

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

An app to do a population receptive field analysis on HCP 7T retinotopy fMRI data

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

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).

Preprocessing and reconstruction of diffusion MRI

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A sample brainlife app that uses EEG data (fif)

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.

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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...

Configurable Pipeline for the Analysis of Connectomes

Generate connection matrix for BIDS directories

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