485 Works

Track the Human Optic TRAct (THOTRA) - Trekker - v1.0

Brad Caron, , Franco Pestilli & Soichi Hayashi
This app uses [Trekker](https://dmritrekker.github.io) to Track the Human Optic Tract.

Trekker ROI Tracking (dtiinit)

Brad Caron, , Franco Pestilli & Soichi Hayashi
This app uses [Trekker](https://dmritrekker.github.io) to track between multiple ROIs.

Track the Human Optic TRAct (THOTRA) - Trekker (dtiinit)

Brad Caron, , Franco Pestilli & Soichi Hayashi
This app uses [Trekker](https://dmritrekker.github.io) to Track the Human Optic Tract.

Temporary converter app from NODDI-deprecated to NODDI datatype

Brad Caron
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Track The Human Optic RAdiation (THORA): Trekker - Eccentricity - DEPRECATED

Brad Caron
This app uses [Trekker](https://dmritrekker.github.io) to Track the Human Optic Radiation.

Convert visualizer of OR to all streamlines (temp)

Brad Caron
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Convert network neuro matrix to conmat

Brad Caron
This app will converts a network matrix of a measure of interest (i.e. density, count) found in the raw:networkmatrices datatype output of Network Neuro app and a parcellation used to generate the matrix to a conmat datatype. This is a temporary app until the Network Neuro app outputs a conmat datatype. This conmat datatype is main datatype for a majority of the network processing apps currently on the website. May be deprecated in the future.

Generate images of DWI

Brad Caron
Create mid-axial, sagittal, and coronal slice png of DWI image

Track The Human Optic RAdiation (THORA): Trekker - Eccentricity - Testing

Brad Caron
This app uses [Trekker](https://dmritrekker.github.io) to Track the Human Optic Radiation.

Segment white matter tracts using pyAFQ

Brad Caron
This app will segment a whole-brain tractogram into the 20 whole-brain tracks provided by Automatic Fiber Quantification (AFQ). This app takes a dwi, track/tck, and freesurfer inputs and outputs a white-matter classification (WMC) structure containing the names and streamlines indices of the AFQ tracks.

Generate images of tissue type masks

Brad Caron
Create mid-axial, sagittal, and coronal slice png of tissue type masks. If you include a T1, the pngs will display an outline of the different masks on the T1. Else, the pngs will be of binary masks of the different tissue types: gray matter, white matter, CSF, and gray matter white matter interface.

Plot response function

Brad Caron & Paolo Avesani
Generate a png image of the response function from CSD projected onto a sphere. This code was originally written by Paolo Avesani for the O3D Nature Scientific Data paper (code: https://github.com/brain-life/o3d-code/blob/master/figures/plot_response.py; paper: https://www.nature.com/articles/s41597-019-0073-y)

Mrtrix3 iFOD2 ROI Tracking (dwi)

Brad Caron
This app will generate multiple ROI to ROI tractograms using mrtrix3's probabilistic iFOD2 algorithm and anatomically constrained tractography framework (ACT).

combineROI

Sophia Vinci-Booher
This app will combine two ROI datatype datasets into one ROI datatype dataset. If, for example, there are 3 rois in the first ROI dataset and 2 rois in the second ROI dataset, the output ROI data set will contain 5 rois. NOTE: This app can be used to extract one roi from an ROI dataset. If you enter the same roi in the roi1 and roi2 fields, the resulting ROI will simply be that...

Trekker ROI Tracking (dwi) - v1.0

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

Intersect Tracts with ROI

Brad Caron
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ROI to ROI Tracking - MRTrix 0.2.12

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).

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

FreeSurfer Postprocessing

Brent McPherson
The converts labeled volumes to .nii.gz, creates white matter and corpus callosum masks, performs alignment to MNI space, and creates a 278 cortical labeled volume from Shen et al. 2013.

HD-BET

Anibal Solon Heinsfeld
HD-BET is an automated brain extraction method for MRI using neural networks.

fMRIPrep - Volume Output

Daniel Levitas, David Hunt, Josh Faskowitz & Soichi Hayashi
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

Linearly align DWI to another DWI with FSL Flirt

Brad Caron
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Independent evaluation of the reliability of major human white matter tracts mapped via brainlife.io

Franco Pestilli, Jan Kurzawski & Kyriaki Mikellidou
Test data

Independent evaluation of the reliability of major human white matter tracts mapped via brainlife.io

Franco Pestilli, Jan Kurzawski & Kyriaki Mikellidou
Retest data

dsi-studio-tt2trk

Convert TRK format to TinyTrack format

Registration Year

  • 2021
    2
  • 2020
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  • 2019
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  • 2018
    140

Resource Types

  • Software
    484
  • Service
    1

Affiliations

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