215 Works

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

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).

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.

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.

TractSeg test

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

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.

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 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.

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.

Ensemble Tracking with dtiInit

Lindsey Kitchell, Franco Pestilli, Brent McPherson & Brad Caron
This service uses MRtrix 0.2.12 to do ensemble tracking using tensor and constrained spherical deconvolution (csd) algorithms. It generates a large set of candidate streamlines using a tensor-based deterministic model, csd-based deterministic model, and csd-based probabilistic model. The csd-based models can be computed at lmax values of 2, 4, 6, 8, 10, and 12. All candidate streamlines are combined into a single track.mat file. If you know the max lmax value for your data input...

MRtrix2 Tracking with dtiInit

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service uses mrtrix 2.0 to track using three methods DTI-based Deterministic, CSD-based Probabilistic and Deterministic. It generates three separate tractograms (TCK), one for each algorithm.

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.

dtiInit

Soichi Hayashi, Paolo Avesani, Lindsey Kitchell & Franco Pestilli
Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1

DWI preproc and nonlinear registration to T1

Kate Alpert
App for running mrtrix3 dwipreproc and then performing nonlinear registration of dwi to T1 (by running ANTs affine+nonlinear registration of CSF masks of mean b0 and T1). Bvectors are rotated with the affine transform. App is recommended for bringing dwi to T1 space if no phase encoding contrast between b=0 images was collected (so mrtrix3 dwipreproc cannot perform inhomogeneity field estimation).

AFQ Tract Classification

Soichi Hayashi & Lindsey Kitchell
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...

DP Remove Tracts with dtiInit

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs Gen_niftis_remove_tracts

Registration Year

  • 2018
    139
  • 2019
    76

Resource Types

  • Software
    215

Data Centers

  • Brainlife Production
    215