214 Works

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)

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.


Soichi Hayashi & Franco Pestilli
Brainlife.io tutorial App

CSA Peaks

Aman Arya
This service generates a csa model using dipy from a given dwi file and freesurfer mask. It then saves the evaluated peaks of the csa model into a dipy compatible .pam5 (peaks and models 5) file type for use in other dipy applications and scripts.

Network Matrices

Brent McPherson
create connectivity graphs from streamline tractography.

Tractography quality check

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

Open Diffusion Data Derivatives

Soichi Hayashi, Paolo Avesani & Franco Pestilli
Open Diffusion Data Derivatives (O3D). Reproducible Neuroimaging via open cloud services: Data upcycling to advance discovery in brain science

DWI preproc and nonlinear registration to T1

Kate Alpert
App for running mrtrix3 dwipreproc and then performing nonlinear registration of dwi to T1 (by running ANTs affine+nonlinear registration of CSF masks of mean b0 and T1). Bvectors are rotated with the affine transform. App is recommended for bringing dwi to T1 space if no phase encoding contrast between b=0 images was collected (so mrtrix3 dwipreproc cannot perform inhomogeneity field estimation).

HCP Pipeline

Soichi Hayashi
Run HCP Pipeline powered by BIDS app

Convert wmc to multiple trk

Soichi Hayashi & Paolo Avesani
Takes a white matter classification resulting from a tract segmentation app and outputs one trk file for each segmented tract.


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

Bias Field Correction (dwi)

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

3D Tract Surfaces

Lindsey Kitchell
app to generate surfaces of each fiber tract

Posterior Associative White Matter Tracts Segmentation

Franco Pestilli & Daniel Bullock
This brainlife.io App implements the white matter segmentation of the vertical tracts described in Bullock et al. 2019. It segments 8 (4 per hemisphere) white matter tracts, the posterior Arcuate (pArc), temporal-parietal connection (TPC), middle-longitudinal fasciculus (MdLF-SPL MdLF-Ang) and the vertical occipital fasciculus (VOF).

BHCK Tutorial

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

AnalyzepRF on HCP data

David Hunt
An app to do a population receptive field analysis on HCP 7T retinotopy fMRI data

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

Segment tracts between multiple brain regions from atlas

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

Plot Eigenfunctions

Lindsey Kitchell
App to plot the eigenfunctions of the Laplace Beltrami Spectrum.

FSL Top-up & Eddy

Brad Caron
This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.

Registration Year

  • 2018
  • 2019

Resource Types

  • Software

Data Centers

  • Brainlife Production