485 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.

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.

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....

Freesurfer Deface

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca

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.

dev-ensembletracking

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

brainlife/app-stage

Soichi Hayashi
To monitor app-stage

Remove Tract Outliers

Daniel Bullock
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Convert wmc to trk

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

wmaSeg - Giulia's patch

Giulia Berto
Classifies streamlines into known anatomical tracts.

app-repeat-tracking-osg

Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

Convert tck to trk in T1 space

Soichi Hayashi & Paolo Avesani
Convert a tractogram in tck format to a trk format file in T1 space

fMRI to Connectivity Matrices

Soichi Hayashi & Josh Faskowitz
fmriprep outputs to connectivity matrices

multi-LAP and multi-NN with trk

Giulia Berto
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).

multi-LAP and multi-NN (deprecated)

Giulia Berto
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP). It also performs Nearest Neighbor (NN, or multi-NN) segmentation for comparison. WARNING: This App was used specifically for a Reproducibility Study and has been deprecated.

DSC evaluation (mask - mask)

Giulia Berto
Compute the degree of overlap between two bundle masks using the Dice Similarity Coefficient (DSC) score.

DP Remove Tracts with DWI

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

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.

Laplace Beltrami Spectrum: Eigenvalues and Eigenvectors

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

Generate ROIs from an atlas

Franco Pestilli & Daniel Bullock
Generates specified ROIS (in nifti format) from an input atlas.

analyzePRF on HCP data (Surface)

David Hunt
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mergeDWI

Sophia Vinci-Booher
Concatenates one or more diffusion images.

Generate images of DWI overlaid on T1

Brad Caron
Create mid-axial, sagittal, and coronal slice png of T1 image with DWI outline overlayed

Cortex Tissue Mapping (Native & Template Space)

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

Create brainmask of DWI using MrTrix3

Brad Caron
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Registration Year

  • 2021
    2
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    484
  • Service
    1

Affiliations

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