205 Works

Generate images of data mapped to cortical surface

Brad Caron
This app will generate images (jpgs) of data mapped to the cortical surface using MNE-python's (https://mne.tools/stable/index.html) build of pysurfer (https://pysurfer.github.io/index.html).

Parcellation Statistics - Surface

Brad Caron
This app will convert important parcellation statistics, including volume of each individual ROI given in a parcellation. These can be used for group analyses. This app should be used whenever possible to compute parcellation statistics (uses freesurfer's mri_annotation_stats).

FC Identifiability/Fingerprinting Analyses

App on processing, analyzing eFC

Segment tracts into multiple bundles using QuickBundles

Brad Caron
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Conmat 2 Network

Simple brainlife app to create a network from a conmat matrix.

C-PAC

Anibal Solon Heinsfeld, Brad Caron, Cameron Craddock, Franco Pestilli, Giulia Berto, Jon Clucas, Soichi Hayashi &
This is the official C-PAC (Configurable Pipeline for the Analysis of Connectomes) brainlife.io app. Currently this app runs either the default pipeline or one of our preconfigured pipelines.

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

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.

Track the Human Optic RAdiation (THORA) - Trekker (V2)

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

CBIG

Elijah Christopher Baughan
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Tractogram Filtering

Paolo Avesani & Pietro Astolfi
Filtering out of artifactual streamlines from a tractogram with a geometric deep learning model

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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pRFLife with mrTools

David Hunt
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mergeROI

Sophia Vinci-Booher
This app will merge two rois within an ROI datatype dataset into one ROI. The user must specify which two rois should be merged. The app will output one roi that contains all of the voxels that were in the two original rois.

FSL Anat (T2)

Brad Caron
This app will perform fsl_anat (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat)

Trekker ROI Tracking (DWI)

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

bold time series

Josh Faskowitz
an app to get nuisance regressed time series from a preprocessed bold, confounds, and a parc

Collegiate athlete brain data for white matter mapping and network neuroscience

Brad Caron & Franco Pestilli
We present diffusion and anatomical (T1w) processed data and derivatives from a group of IU athletes (football, cross-country) and non-athletes (students). The raw data contains both anatomical (T1 weighted) and diffusion-weighted (dMRI) magnetic resonance imaging data. The processed data shares 14 types of derivatives across 42 participants, comprising of 84 brainmasks (2 per participant), 42 Freesurfer outputs (1 per participant), 168 fiber orientation dispersion (FOD) images (4 per participant), 588 diffusion parameter maps (14 per...

Extract DWI volumes of choice

Brad Caron
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Compile tract profiles to summary structure

Brad Caron
This app will the individual tract tract profiles csv’s from the tractprofile dataype into a single summary csv for group analysis and machine learning. This app takes in a tractprofile datatype. The app will output a csv entitled ‘tracts.csv’ that can be used for group statistics and machine learning.

Track the Human Optic RAdiation - mrtrix3 iFOD2 (dtiinit)

Brad Caron
This app will generate optic radiations using MrTrix3's iFOD2 algorithm with the capability of using the Anatomically Constrained (ACT) framework

Make white matter mask in dwi space from Freesurfer (dtiinit)

Brad Caron
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dsi-studio-dwi2src

DSI Studio scripts converting DWI file to SRC format.

Registration Year

  • 2020
    205

Resource Types

  • Software
    204
  • Service
    1

Affiliations

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