507 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).

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

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.

White Matter Anatomy Segmentation

Daniel Bullock
Classifies streamlines into known anatomical tracts.

Fit MAPMRI

Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Fit MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng. Either the laplacian or positivity or both must be set to True. (dipy_fit_mapmri)

dt6 To Nifti Converter

Soichi Hayashi & Brad Caron
Will take a dt6 and create tensor (FA,MD,AD,RD) and Westin Shape Indices (cl, cp, cs) nifti images from a dt6.mat structure.

dtiInit

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

Fit DTI

Aman Arya, Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Tensor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)

DWI Info

Franco Pestilli, Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Provides useful information about different files used in medical imaging.

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Diffusion Predictor Grid Search (AppA)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

White Matter Mask

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.

Noddi Amico - Deprecated

Brad Caron
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs) and an optional brainmask of the DWI. Will output the four NODDI output files: neurite density index (ndi), orientation dispersion index (odi), isotropic volume fraction (isovf), and the directions (dirs).

LAP from 5 examples

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

WMC to TRK conversion and resample

Giulia Berto
Code to convert wmc to trk and resample with the given step size.

Dtiinit Datatype Conversion

Brad Caron
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Trekker ROI Tracking

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

Brad Quals

Brad Caron
Datasets and derivatives generated for Brad Caron's Qualifying exams.

Registration Year

  • 2021
    23
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    506
  • Service
    1

Affiliations

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