468 Works

Ensemble Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell, Brent McPherson & Brad Caron
This App creates a large set of candidate streamlines using an ensemble of algorithms and parameter values. All outputs will be then combined into a single track.tck output.

old ensemble tracking

Lindsey Kitchell & Brad Caron
This App creates a large set of candidate streamlines using an ensemble of algorithms and parameter values. All outputs will be then combined into a single track.tck output.

NODDI Amico (single shell) - Deprecated

Brad Caron
This fits the NODDI model on single shell data. The only value that should be trusted is orientation dispersion (OD), as this measure can be fit accurately with single shell data

dt6 To Nifti Converter

Soichi Hayashi & Brad Caron
Will take a dt6 and create tensor (FA,MD,AD,RD) and Westin Shape Indices (cl, cp, cs) nifti images from a dt6.mat structure.

Fit MAPMRI

Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Fit MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng. Either the laplacian or positivity or both must be set to True. (dipy_fit_mapmri)

Fit DTI

Aman Arya, Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Tensor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)

CBIG

Elijah Christopher Baughan
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White Matter Anatomy Segmentation

Daniel Bullock
Classifies streamlines into known anatomical tracts.

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Laplace Beltrami Spectrum: Eigenvalues and Eigenvectors

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum and Eigenvectors using Matlab.

Generate tract endpoint maps

Daniel Bullock
This app will generate endpoint maps for all tracts in an input classification structure. User can specify what sort of decay/smoothing algorithm can be used (or none).

brainlife/app-stage

Soichi Hayashi
To monitor app-stage

Convert wmc to trk

Paolo Avesani
Convert a white matter classification (wmc) structure to a tractogram as a single trk file

WMC Figures (AFQ or WMA)

Brad Caron & Lindsey Kitchell
This service creates 4 figures of each AFQ tract: axial, left sagittal, right sagittal, coronal. Please choose the t1 image slices you would like displayed. The default slices work well for the HCP t1 images if they have not been re-ACPC aligned. If you have ACPC aligned your t1 images using the ACPC alignment app on Brain Life the following values are a good starting point: coronal = 105, sagittal = 89, axial = 65....

dev-ensembletracking

Brent McPherson
copy of ensemble tracking that runs from the master branch for testing new changes

Tractography quality check (trk)

Daniel Bullock
A quality check application for tractography, segmentatations, and LiFE structures. For the whole brain tractogram, provides a number of statistics associated with average streamline characteristics (i.e. count, volume occupied, avg length, length distribution). Does the same for the positively weighted streamlines of an FE structure if input. If a classification structure is input, provides a number of macrostructural statistics like stream count, volume, avg length, whole brain count/volume proportion, etc).

Brad Quals

Brad Caron
Datasets and derivatives generated for Brad Caron's Qualifying exams.

Trekker ROI Tracking

Brad Caron, & Soichi Hayashi
Brainlife App (wrapper) for dMRI based fiber tracking between ROIs using parallel transport tractography

hello-world

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Segment tractogram into fiber categories

Daniel Bullock & Soichi Hayashi
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).

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

Brad Caron & Soichi Hayashi
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LAP from 5 examples

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

Dtiinit Datatype Conversion

Brad Caron
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DP Fit Model with dtiInit

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.

Diffusion Predictor Grid Search (AppA)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

Registration Year

  • 2020
    190
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    467
  • Service
    1

Affiliations

  • The University of Texas at Austin
    4
  • Indiana University
    3