686 Works

[WIP] Create animation from trk

Soichi Hayashi
Generate animation of trk streamlines

Tract Analysis Profiles - Myelin mapping

Brad Caron
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

MNE-BIDS-Pipeline: [2] MEEG sensor analysis

Julia Guiomar Niso Galan
This Brainlife App analyses MEG (and EEG) data at the sensor-level using MNE-BIDS-Pipeline (https://mne.tools/mne-bids-pipeline).

HD-BET

Anibal Solon Heinsfeld
HD-BET is an automated brain extraction method for MRI using neural networks.

Generate images of tissue type masks

Brad Caron
Create mid-axial, sagittal, and coronal slice png of tissue type masks. If you include a T1, the pngs will display an outline of the different masks on the T1. Else, the pngs will be of binary masks of the different tissue types: gray matter, white matter, CSF, and gray matter white matter interface.

FSL Brain Extraction (BET) on fMRI

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Brain Extraction via FSL's BET command

Open Diffusion Data Derivatives

Soichi Hayashi, Paolo Avesani & Franco Pestilli
Open Diffusion Data Derivatives (O3D). Reproducible Neuroimaging via open cloud services: Data upcycling to advance discovery in brain science

Convert ctf file to fif

Aurore Bussalb & Maximilien Chaumon
Convert ctf files into fif format

Cortex Tissue Mapping (Native & Template Space) - qMRI

Brad Caron
This app will map volumated measure files (i.e. qmri) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

ANTsRegistration

Eva Bacas
registering t1w images with ANTs

Structural Networks (count)

Brent McPherson &
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Compute average cortexmap data for group analysis

Brad Caron
This app will compute average surfaces and cortexmap data for group anaylsis

Structural Networks (Microstructure Properties - Tensor)

Brent McPherson
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Structural Connectome MRTrix3 (SCMRT) (SIFT2)

Brad Caron
Generate structural connectomes using MRTrix3 and SIFT2

pRFs / Benson14-Retinotopy

Brad Caron & David Hunt
Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

Generate ROIs in DMRI Space with WM Skeleton mask

Brad Caron
This app will generate ROIs from a parcellation, subcortical structures found in the Freesurfer aseg, cortical structures found in the Freesurfer parcellations, and population receptive field visual area segmentations. The ROIs will be resliced into diffusion space in of this, merging ROIs is allowed.

Connectivity Gradients

Anibal Solon Heinsfeld
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Structural Networks (Microstructure Properties - NODDI)

Brent McPherson
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Network Tensor Tract Profiles

Brent McPherson
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HCP Pipeline test app

David Hunt
testing volume and surface fMRI pipelines with fmaps

Merge Tractography (tcks) together with MRTrix3 (Two Tcks)

Brad Caron
This is copy of the mergeTCK BL app (https://doi.org/10.25663/brainlife.app.219) modified to take two tractograms as input. This is a temporary workaround for the lack of functionality for multi-input datatypes in brainilfe Pipelines.

PyNets

Brad Caron, Derek Pisner, Franco Pestilli, Giulia Berto & Soichi Hayashi
A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

Linearly align DWI to another DWI with FSL Flirt

Brad Caron
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Track the aLIC

Daniel Bullock
Track the anterior limb of the internal capsule with streamline tractography using MRTRIX3

fMRIPrep - Volume Output

Brad Caron, Daniel Levitas, David Hunt, Giulia Berto, Josh Faskowitz & Soichi Hayashi
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

Registration Year

  • 2022
    59
  • 2021
    144
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    685
  • Service
    1

Affiliations

  • The University of Texas at Austin
    4
  • Indiana University
    4