220 Works


Serge Koudoro & Aman Arya
This application takes in a full tractography (Multishell Tractography w/CSA or Multishell Tractography w/ SHORE) and the output from the White Matter Segmentation and uses the Recobundles algorithm to find the corresponding white matter segmentation in the full tractogram.

White Matter Anatomy Segmentation with LiFE (deprecated)

Lindsey Kitchell & Daniel Bullock
Classifies streamlines into known anatomical tracts.

HCP Pipeline (PreFreeSurfer)

Soichi Hayashi & Kate Alpert
BIDS app for HCP pre-FreeSurfer for BrainLife. Performs ACPC alignment, FNIRT-based brain extraction, and bias field correction. (Please see https://github.com/Washington-University/HCPpipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#structural-preprocessing for more information on HCP structural pipelines.)

HCP Pipeline

Soichi Hayashi
Run HCP Pipeline powered by BIDS app

White Matter Segmentation

Aman Arya
This service takes in a nifti and tck output from Multishell Tractography w/ CSA or SHORE and outputs the CST and ILF segmentations in .tck file format of both the left and right hemispheres.

TractSeg HCP (test)

Lindsey Kitchell
Brainlife App for MIC-DKFZ/TractSeg. A tool for fast and accurate white matter bundle segmentation from Diffusion MRI using pretrained pytorch ML model.

Network Neuro

Soichi Hayashi, Paolo Avesani, Franco Pestilli & Brent McPherson
Build structural brain networks using diffusion-weighted MRI, tractography and a brain atlas for cortical and subcortical parcellation.

FSL BET Brain Extraction (DWI)

Lindsey Kitchell & Brad Caron
Brain Extraction via FSL's BET command

Prepare PRF output for visualization

Soichi Hayashi
A brain life app to prepare PRF and freesurfer data to be visualized with ui-3dsurfaces

LAP multiple examples with LiFE

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

Convert Pial (Cortical) and White Matter Surfaces from Freesurfer

Lindsey Kitchell
This application converts Freesurfer's pial and white matter surfaces to different file types. It will convert the lh/rh.pial, lh/rh.white, lh/rh.smoothwm, lh/rh.inflated files into your choice of file type (stl, vtk, gii, mgz)

Generate ROIs from an atlas

Franco Pestilli & Daniel Bullock
Generates specified ROIS (in nifti format) from an input atlas.

HCP ACPC Alignment (T1)

Soichi Hayashi, Brent McPherson & Brad Caron
This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.


Brent McPherson
copy of ensemble tracking that runs from the master branch for testing new changes


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

BHCK Tutorial

Lindsey Kitchell, Franco Pestilli & Brent McPherson
This app is an example for the brainhack 2018 tutorial. Should be deleted

Test Gradient Flip for dtiInit processing

Soichi Hayashi & Lindsey Kitchell
This application will provide a recommendation on which axis you should flip the bvecs of your data, if it is necessary. It will perform fiber tracking using 4 different gradient flip options (no flip, x flip, y flip, and z flip) and report the most likely flip needed for your data. The flip recommendation is made based on the flip direction with the highest number of long fibers.

pRF - Population Receptive Field Analysis

Justin Gardner, Soichi Hayashi, Franco Pestilli & Brad Caron
This app will compute a population receptive field (i.e. pRF) analysis on a given time series. Inputs needed include: a time series nifti, a stimulus nifti, the measurements of the visual stimulus in space (stimimageunits), and dimensions of a mask (mask; optional). Outputs include: x.nii, y.nii, rfWidth.nii and r2.nii. Please see http://gru.stanford.edu/doku.php/mrTools/tutorialsprf for more detail.

Tractography quality check (new wmc input)

Daniel Bullock
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).

Convert tck+dwi to trk (MRtrix 2)

Soichi Hayashi & Lindsey Kitchell
Converts a tck that was made using MRtrix 2 into a trk in the dwi space.

MRtrix2 Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service runs mrtrix 2.0 tracking spanning over multiple tracking methods and parameters (Probabilistic and Deterministic tracking). It generates three separate tracking outputs for each algorithm.

Registration Year

  • 2018
  • 2019

Resource Types

  • Software