215 Works

Track between multiple brain regions from atlas

Franco Pestilli & Daniel Bullock
This app tracks between specified atlas regions to output a set of tracts.


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

Steklov Operator Spectrum

Lindsey Kitchell
app to calculate the Steklov Operator Spectrum on 3D surfaces

Convert brainmask from dtiinit

Brad Caron
temp app to convert brainmask from dtiinit to mask datatype

Compute Volume of Binary Nifti images

Soichi Hayashi & Lindsey Kitchell
computes the volume of binary nifti images


Soichi Hayashi, Serge Koudoro & Aman Arya
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)

White Matter Mask

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

Freesurfer on OSG

Soichi Hayashi
Run freesurfer (v6) on Open Science Grid using fsurf command.

Connectome Evaluator (deprecated by app-life)

Soichi Hayashi
Estimate the quality of your diffusion-weighted data to map human connectomes.

WMC to TRK conversion and resample

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

Tract Profiles

Soichi Hayashi & Aman Arya
This app takes in tracking data from the White Matter Segmentation app well as the nifti files of the user and gives tract profiles for each tracking file in a json format.

ANTs tractogram registration in MNI space

Giulia Berto
ANTs transformation based on T1 and tractogram registration in MNI space


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


Soichi Hayashi
Service that does nothing (exist to do inter-resource transfer)

ROI Generation (w/ dtiinit)

Ilaria Sani & Brad Caron
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).


Soichi Hayashi & Franco Pestilli
Brainlife.io tutorial App

Anatomically-informed multi-LAP

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

Check T1 Orientation

Soichi Hayashi & Lindsey Kitchell
This application checks and reports the orientation (neurological or radiological) of a nifti file.


Soichi Hayashi
Runs MRIQC pipeline (http://mriqc.readthedocs.io/en/stable/reports/smri.html) from Poldrack Lab on selected T1 anatomy.

Generate tract endpoint maps (new wmc Input)

Daniel Bullock
This app will generate endpoint maps for all tracts in an input classification structure. User can specify what sort of decay/smoothing algorithm can be used (or none).


Soichi Hayashi, Sofie Van Den Bossche, Madhur Tandon, Guorong Wu, Franco Pestilli & Daniele Marinazzo
Hemodynamic Response Function Retrieval and Deconvolution (RS-HRF)

Remove First B0 (temp)

Brad Caron
Temporary app to remove first b0 for Athlete Brain Study Dataset

Clean WMC output (deprecated)

Soichi Hayashi, Lindsey Kitchell & Daniel Bullock
(deprecated by Remove Tract Outliers App) This service cleans the output from AFQ and WMA using AFQ's AFQ_removeFiberOutliers function. For more information on the inputs of this application, please read the documentation at the top of the function: https://github.com/yeatmanlab/AFQ/blob/master/functions/AFQ_removeFiberOutliers.m

Registration Year

  • 2018
  • 2019

Resource Types

  • Software

Data Centers

  • Brainlife Production