215 Works

Track between multiple brain regions from ROI directory (new wmc output)

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) rois from an input directory to output a set of tracts.

TractSeg test

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

Segment tracts between multiple brain regions from ROI directory (new wmc output)

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of tracts.

Segment tracts between multiple brain regions from atlas (new wmc output)

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

Segment tracts between multiple brain regions from ROI directory

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of 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.

ROI Generation

Ilaria Sani & Brad Caron
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).

ROI to ROI Tracking

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).

[DIPY] Fit CSA

Soichi Hayashi, Serge Koudoro & Aman Arya
Fits a CSA model to diffusion data (dipy_fit_csa)

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

Plot 3D Surfaces

Lindsey Kitchell
This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.

TractSeg training

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

Trekker

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

Binary Tract Masks

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

Freesurfer on OSG

Soichi Hayashi
Run freesurfer (v6) on Open Science Grid using fsurf command.

Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation

Paolo Avesani & Giulia Berto
A benchmark to test a tract segmentation method that takes into account information about both the underlying anatomy and the geometry of bundles at the same time.

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

DSC evaluation (mask - mask)

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

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

Soichi Hayashi & Josh Faskowitz
fmriprep outputs to connectivity matrices

Tract Analysis Profiles

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

DSC evaluation (wmc - wmc)

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

ACPC alignment via ART

Soichi Hayashi & Lindsey Kitchell
This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.

Registration Year

  • 2018
    139
  • 2019
    76

Resource Types

  • Software
    215