504 Works

LiFE with dtiInit

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell, Paolo Avesani & Soichi Hayashi
LiFE (Linear Fasicle Evaluation) predicts the measured diffusion signal using the orientation of the fascicles present in a connectome. LiFE uses the difference between the measured and predicted diffusion signals to measure prediction error. The connectome model prediction error is used to compute two metrics to evaluate the evidence supporting properties of the connectome.

Posterior Associative White Matter Tracts Segmentation

Brad Caron, Daniel Bullock, Franco Pestilli & Giulia Berto
This brainlife.io App implements the white matter segmentation of the vertical tracts described in Bullock et al. 2019. It segments 8 (4 per hemisphere) white matter tracts, the posterior Arcuate (pArc), temporal-parietal connection (TPC), middle-longitudinal fasciculus (MdLF-SPL MdLF-Ang) and the vertical occipital fasciculus (VOF).

test

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

Bias Field Correction (dwi)

Brad Caron, Franco Pestilli, Lindsey Kitchell & Soichi Hayashi
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm

tutorial-helloworld

Soichi Hayashi & Franco Pestilli
Brainlife.io tutorial App

DP Profile with dtiInit

Soichi Hayashi & Cesar F. Caiafa
Generate FA profiles

Recobundles

Serge Koudoro & Aman Arya
This application takes in a full tractography (Multishell Tractography w/CSA or Multishell Tractography w/ SHORE) and the output from the White Matter Segmentation and uses the Recobundles algorithm to find the corresponding white matter segmentation in the full tractogram.

Check T1 Orientation

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This application checks and reports the orientation (neurological or radiological) of a nifti file.

Check DWI Orientation

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This application checks and reports the orientation (neurological or radiological) of a nifti file.

Check dtiInit Orientation

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This application checks and reports the orientation (neurological or radiological) of a nifti file.

ROI to ROI Tracking - deprecated

Ilaria Sani, Soichi Hayashi, Franco Pestilli & Brad Caron
This app will perform tracking between 2 cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. Inputs include: parcellation (freesurfer; atlas optional) with ROI niftis (generated from app-roiGeneration), 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 other apps on the website (example: Clean WMC Output).

Diffusion Predictor Grid Search (AppA) (old)

Soichi Hayashi
This is an old version that used dwi instead of dtiinit

Clean WMC output

Brad Caron, Daniel Bullock, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
(deprecated by Remove Tract Outliers App) This service cleans the output from AFQ and WMA using AFQ's AFQ_removeFiberOutliers function. For more information on the inputs of this application, please read the documentation at the top of the function: https://github.com/yeatmanlab/AFQ/blob/master/functions/AFQ_removeFiberOutliers.m

AFQ Tract Classification

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This service uses Automated fiber quantification AFQ and fe structure output from LiFE to identify major tract segments and quantify tissue properties along their trajectories. You can choose to have the zero weighted fibers (as determined by LiFE) removed before or after AFQ is applied. useinterhemisphericsplit is a variable from AFQ, which if set to true will cut fibers crossing between hemispheres with a midsaggital plane below z=-10. This is to get rid of CST...

Crop and Reorient T1

Soichi Hayashi & Brad Caron
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

LAP multiple examples with LiFE

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

Volume-based Multiple Linear Regression

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
SOCR / Volume-based Multiple Linear Regression Analysis

Network Matrices

Brent McPherson
create connectivity graphs from streamline tractography.

Tractography quality check

Daniel Bullock
A quality check application for tractography, segmentatations, and LiFE structures

TractSeg training

Pietro Astolfi, Paolo Avesani & Giulia Berto
Automatic White Matter Bundle Segmentation

Trekker - v1.0

Soichi Hayashi, Franco Pestilli, , Brent McPherson & Brad Caron
Brainlife App (wrapper) for dMRI based fiber tracking using parallel transport tractography https://dmritrekker.github.io

AFQ Tract Classification with LiFE

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This service uses Automated fiber quantification AFQ and fe structure output from LiFE to identify major tract segments and quantify tissue properties along their trajectories. You can choose to have the zero weighted fibers (as determined by LiFE) removed before or after AFQ is applied. useinterhemisphericsplit is a variable from AFQ, which if set to true will cut fibers crossing between hemispheres with a midsaggital plane below z=-10. This is to get rid of CST...

Human white matter microstructure predicts elite sports participation

Franco Pestilli & Brad Caron
Collision-sport athletes, especially football players, are exposed to a higher number of repetitive head impacts. Little is known, however, regarding the effects of long-term exposure to repetitive head impacts on brain tissue structure and the locations (i.e. superficial or deep tissue structures) affected. On top of this, little is known about the effects of highly competitive athletics on brain tissue structure. We investigated this relationship, including the baseline effect of collegiate athletic participation, by mapping...

Binary Tract Masks

Lindsey Kitchell & Soichi Hayashi
app to generate binary masks of the segmented fiber tracts

Segment tracts between multiple brain regions from atlas

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified atlas regions to output a set of tracts.

Registration Year

  • 2021
    21
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    503
  • Service
    1

Affiliations

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