216 Works

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

Cortex Tissue Mapping

Brad Caron
This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

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.

AFQ Tract Classification with LiFE

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
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...

Noddi Amico (w/ dtiinit)

Brad Caron
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs), and the single shell dwi file that has been aligned to the subject's T1 (i.e. dtiinit output) as input. The app will align the multi-shell data to the single-shell data...

Convert tck to trk in DWI space

Paolo Avesani
Convert a tractogram in tck format to a trk format file in dwi space

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.

Map pRFs in visual cortex with anatomy

David Hunt
Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

Convert trk to tck

Soichi Hayashi
Convert trk (trackvis) file to tck (mrtrix) format

Check DWI Orientation

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

Connectome Mapper

David Hunt
Generate connection matrix for BIDS directories

BIDS Mrtrix3 Connectome

Kate Alpert
BIDS app for Mrtrix3 Connectome DTI processing for BrainLife. Generates subject connectomes from raw image data using tools provided in the *MRtrix3* software package. http://www.mrtrix.org/. Optional preprocessing includes FSL's topup analysis for spatial correction and requires at least 2 input DTI images.

Connectome Mapper for BIDS datasets

David Hunt
Generates connectome matrices and for T1 and BIDS datasets

Freesurfer 6.0

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service allows you to submit T1 anatomical image and process it using Freesurfer, which is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. Please consider using OSG version to process a large number of subjects

Vistasoft DWI T1 Registration

Brad Caron
This app will register a DWI image to a T1w image and rotate the bvecs. Requires a DWI image (with bvals and bvecs) and an T1w image (either ACPC-aligned or native). Will output an aligned DWI image, the rotated bvecs, and the bvals files.

Tensor Mask

Soichi Hayashi, Serge Koudoro & Aman Arya
generate a mask from FA


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


Soichi Hayashi, Serge Koudoro & Franco Pestilli
Fit a Diffusion Kurtosis Imaging model to multishell Diffusion-weighted data (dipy_fit_dki)

Registration Year

  • 2018
  • 2019

Resource Types

  • Software