236 Works

Tractography quality check

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).

Bias Field Correction (dwi)

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

ANTs transformation and wmc registration with FA

Giulia Berto
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.


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

Non Local Means Denoising

Serge Koudoro
Brainlife wrapper app for Dipy workflows.

White matter tracts statistics and quality control

Franco Pestilli & Daniel Bullock
This brainlife.io App will compute aggregrate statistics on the white matter tracts produced on brainlife.io. Statistics such as fiber count, tract volume, etc can be used to compare across tracts, across subjects either for scientific analyses or quality control of the results.

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.

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).

Connectome Evaluator

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


Serge Koudoro
RecoBundles - Automatic extraction of brain pathways

DP Remove Tracts with dtiInit

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs Gen_niftis_remove_tracts

mrtrix3 preprocess

Brent McPherson
Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided.

Generate Equivolumetric Surfaces

David Hunt
Computes n equally spaced offset surfaces between the white and pial surfaces with equal ratios between areas of successive surfaces, which samples the same layers in gyri and sulci.

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.

Tractography quality check

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

Plot 3D Surfaces

Lindsey Kitchell
This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.


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

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.

FSL Brain Extraction (BET) on DWI

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

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.)

Track between multiple brain regions from ROI directory

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

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).

Registration Year

  • 2018
  • 2019

Resource Types

  • Software