485 Works

Extract diffusion metrics inside ROIs (DTI)

Brad Caron
This app will extracts diffusion metrics (tensor) from within ROIs for ROI-level analysis using FSL. Will output metric x ROI NIFTI images. Takes in DWI, tensor, NODDI, and ROIs inputs and outputs a directory with the metric x ROI NIFTI images. Inflation can be performed on the ROIs using SPM.

Strength of evidence for white-matter tracts

Franco Pestilli & Soichi Hayashi
Compute the strength of evidence for white matter tracts in a classification given the measured diffusion-weighted MRI data

Time Series to Network

Josh Faskowitz
convert an NxT time series to an NxN functional connectivity matrix

Generate ROIs in DMRI Space (dtiinit)

Brad Caron
This app will generate ROIs from a parcellation, subcortical structures found in the Freesurfer aseg, cortical structures found in the Freesurfer parcellations, and population receptive field visual area segmentations. The ROIs will be resliced into diffusion space in of this, merging ROIs is allowed.

Generate images of mask overlaid on DWI

Brad Caron
Create mid-axial, sagittal, and coronal slice png of the brainmask overlaid on the DWI image

app app

David Hunt
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Network Visualization

This app generates simple 2D static visualizations for networks by using a force-directed algorithm. The current implementation uses the Large Graph Layout (LGL) algorithm.

merge2TCKs - copy

Brad Caron
This is copy of the mergeTCK BL app (https://doi.org/10.25663/brainlife.app.219) modified to take two tractograms as input. This is a temporary workaround for the lack of functionality for multi-input datatypes in brainilfe Pipelines.

Generate ROIs for Visual White Matter Tracking in dMRI Space (Benson pRF)

Brad Caron
This app will generate ROIs that can be used for visual white matter tracking, including optic radiation tracking. This includes V1 from a pRF visual area segmentation, the left and right LGNs from a thalamic nuclei segmentation, and exclusion ROIs from freesurfer. The ROIs will be resliced into diffusion space in of this.

Trekker ROI Tracking (dtiinit)

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

Tract Analysis Profiles (NODDI)

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

Extract diffusion metrics inside tissue types

Brad Caron
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Generate images of NODDI

Brad Caron
Create mid-axial, sagittal, and coronal slice pngs of the NODDI

Map pRFs in visual cortex with anatomy - copy

David Hunt
Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

HCP-minor bundle dataset

Giulia Berto
Dataset of expert-based segmented white matter bundles connecting the human dorsal and posterior cortices. The bundles included in this dataset are: the posterior arcuate fasciculus (pArc), the temporo-parietal connection to the superior parietal lobule (TP-SPL), the middle longitudinal fasciculus–superior parietal lobule component (MdLF-SPL), and the middle longitudinal fasciculus–superior angular gyrus component (MdLF-Ang).

Mrtrix2 CSD

Brad Caron
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DenseUnet-based Automatic Rapid Tool for brain Segmentation (DARTS)

David Hunt
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Extract multi-tcks from wmc + wbfg or composite tck

Daniel Bullock
This application takes an input tractography amalgum (i.e. whole brain fiber group (WBFG) or composite) and, using the categories designated in the White Matter Category (WMC) input, extracts and outputs a tck file for each category into the output directory. Intended to facilitate users performing analyses offline/outside of the brainlife platform. WARNING: Submitting mismatched input TCK and WMC will result in an error, but may also result in garbage output in the event that the...

pyAFQ_dry_run

John Kruper
Automated Fiber Quantification ... in Python

Tracking the Visual White Matter (TVWM) (Trekker) - Eccentricity

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

Cortex Tissue Mapping - Fukutomi et al 2018 Replication

Brad Caron
This application is a port of the NODDI Cortex Mapping code (https://github.com/RIKEN-BCIL/NoddiSurfaceMapping) developed by Fukutomi et al. The description of methodologies can be found in their 2018 Neuroimage paper (https://www.sciencedirect.com/science/article/pii/S1053811918301058?via%3Dihub). If used, please cite: Fukutomi, H., Glasser, M.F., Zhang, H., Autio, J.A., Coalson, T.S., Okada, T., Togashi, K., Van Essen, D.C., Hayashi, T., 2018. Neurite imaging reveals microstructural variations in human cerebral cortical gray matter. Neuroimage.

dsi-studio-dwi2src

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Track The Human Optic RAdiation (THORA): Trekker - Eccentricity (V2)

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

Tract Analysis Profiles - copy

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

Development of white matter tracts between and within the dorsal and ventral streams

Sophia Vinci-Booher
This is data related to the upcoming article by Vinci-Booher et al. The dataset contains diffusion-weighted and T1-weighted magnetic resonance imaging from 24 children (age 4.5-9 years of age) and 12 adults (18-21 years of age).

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