224 Works

ACPC alignment via ART

Soichi Hayashi & Lindsey Kitchell
This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.


Soichi Hayashi, Serge Koudoro & Aman Arya
Fits a CSA model to diffusion data (dipy_fit_csa)


Soichi Hayashi & Franco Pestilli
Brainlife.io tutorial App

Connectome Mapper

David Hunt
Generate connection matrix for BIDS directories

Crop and Reorient T1

Soichi Hayashi & Brad Caron
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

Remove First B0 (temp)

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

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.

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.


Soichi Hayashi, Serge Koudoro & Aman Arya
Fit a CSD model to diffusion data (dipy_fit_csd)

fMRI to Connectivity Matrices

Soichi Hayashi & Josh Faskowitz
fmriprep outputs to connectivity matrices

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.

Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation

Paolo Avesani & Giulia Berto
A benchmark to test a tract segmentation method that takes into account information about both the underlying anatomy and the geometry of bundles at the same time.


Soichi Hayashi, Serge Koudoro & Aman Arya
Tesor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)

Segment tracts between multiple brain regions from atlas (new wmc output)

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified atlas regions to output a set of tracts.

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

Enhanced Ensemble Tractography

Brad Caron & Brent McPherson
Performs ensemble tractography with MRTrix 0.2.12 with user specified values for lmax and curvatures across probabilistic, deterministic, and tensor methods. Additionally, it seeds and tracts extra streamlines through the corpus callosum.

Freesurfer Group Analysis

Soichi Hayashi
Do some basic group analysis on freesurfer outputs

HCP Pipeline (FreeSurfer)

Kate Alpert
BIDS app for HCP FreeSurfer for BrainLife. Requires T1w_acpc_dc_restore.nii.gz, T1w_acpc_dc_restore_brain.nii.gz, and T2w_acpc_dc_restore.nii.gz from PreFS pipeline. (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.)

Bias Field Correction (anat/t1w)

Soichi Hayashi & Lindsey Kitchell
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm

Segmentation with Median Otsu

Soichi Hayashi & Serge Koudoro
Brain segmentation with the median_otsu method using DIPY. Default parameters work well on most volumes but you can play with them if needed

Check DWI Orientation

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

Track between multiple brain regions from atlas

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

Registration Year

  • 2018
  • 2019

Resource Types

  • Software