138 Works

Convert wmc-deprecated to wmc

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
App to convert the old wmc-deprecated datatype to the new wmc datatype

Generate tract endpoint maps

Daniel Bullock

ROI Generation (thalamic nuclei)

Brad Caron
Generate a parcellation volume (and roi nifti files split into each label) for specific ROIs, or every ROI, for a parcellation from freesurfer output and/or input parcellation volume. This App can also inflate input parcellation volume toward non-white matter voxels.

Steklov Operator Spectrum

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

Decimate and/or Convert 3D surfaces

Lindsey Kitchell
This application will reduce the number of vertices and faces on 3D surfaces by the percent reduction chosen. It can also be used to convert between filetypes.

Align DWI to Dtiinit

Soichi Hayashi & Brad Caron
This app will align a DWI datatype to the output from DTIInit. This may be necessary if a user is using DTIInit purely for the anatomical alignment and the input dataset contains multi-shell data.

Convert brainmask from dtiinit

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


Sophia Vinci-Booher
Merge multiple TCK files into one TCK file.


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

multi-LAP with trk

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

Freesurfer on OSG

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


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

Knowing-what-you-know in brain segmentation - copy

Nikhil Goyal

Align HCP to Native Space

David Hunt
Aligns HCP fMRI volume data in MNI space to subject space

WMA Tract Segmentation with ROIs

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of tracts.

Tractography quality check

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
A quality check application for tractography, segmentatations, and LiFE structures. For the whole brain tractogram, provides a number of statistics associated with average streamline characteristics (i.e. count, volume occupied, avg length, length distribution). Does the same for the positively weighted streamlines of an FE structure if input. If a classification structure is input, provides a number of macrostructural statistics like stream count, volume, avg length, whole brain count/volume proportion, etc).

Connectome Mapper for BIDS datasets

David Hunt
Generates connectome matrices and for T1 and BIDS datasets

Automated Segmentation of Hippocampal Subfields (ASHS)

Franco Pestilli, Giulia Berto, Soichi Hayashi & Sophia Vinci-Booher
brainlife.io app for using Automated Segmentation of Hippocampal Subfields (ASHS) software to segment hippocampal subfields based on previously acquired atlases

FSL Brain Extraction (BET) on fMRI

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Brain Extraction via FSL's BET command

Tractography quality check

Daniel Bullock
A quality check application for tractography, segmentatations, and LiFE structures

TractSeg training

Pietro Astolfi, Paolo Avesani & Giulia Berto
Automatic White Matter Bundle Segmentation

Trekker - v1.0

Soichi Hayashi, Franco Pestilli, , Brent McPherson & Brad Caron
Brainlife App (wrapper) for dMRI based fiber tracking using parallel transport tractography https://dmritrekker.github.io

AFQ Tract Classification with LiFE

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This service uses Automated fiber quantification AFQ and fe structure output from LiFE to identify major tract segments and quantify tissue properties along their trajectories. You can choose to have the zero weighted fibers (as determined by LiFE) removed before or after AFQ is applied. useinterhemisphericsplit is a variable from AFQ, which if set to true will cut fibers crossing between hemispheres with a midsaggital plane below z=-10. This is to get rid of CST...

Human white matter microstructure predicts elite sports participation

Franco Pestilli & Brad Caron
Collision-sport athletes, especially football players, are exposed to a higher number of repetitive head impacts. Little is known, however, regarding the effects of long-term exposure to repetitive head impacts on brain tissue structure and the locations (i.e. superficial or deep tissue structures) affected. On top of this, little is known about the effects of highly competitive athletics on brain tissue structure. We investigated this relationship, including the baseline effect of collegiate athletic participation, by mapping...

Registration Year

  • 2019

Resource Types

  • Software