188 Works

Diffusion Predictor Grid Search (AppA)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

White Matter Anatomy Segmentation (for Dan Bullock's Paper)

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

Tract Analysis Profiles

Brad Caron
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

Tract Analysis Profiles_deprecated

Brad Caron
This app has been deprecated. It will only work with wmc_deprecated datatype.

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)

Decimate 3D surfaces

Lindsey Kitchell
This application will reduce the number of vertices and faces on 3D surfaces by the percent reduction chosen.

Freesurfer Group Analysis

Soichi Hayashi
Do some basic group analysis on freesurfer outputs

Segment tractogram into fiber categories

Franco Pestilli & Daniel Bullock
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).


Soichi Hayashi & Franco Pestilli
Brainlife.io tutorial App

Mouse Segmentation Pipeline

Soichi Hayashi, Lei Wang & Kate Alpert
Pipeline for mouse brain skull-stripping and ROI segmentation

Deprecated - Laplace Beltrami Spectrum

Lindsey Kitchell
This application will calculate the Laplace Beltrami spectrum of 3D surfaces in the .vtk file format using the LBS function provided with Mindboggle (http://www.mindboggle.info/). This application computes the Laplace-Beltrami spectrum using a linear finite element method, following the definitions and steps given in Reuter et al.'s 2009 paper: "Discrete Laplace-Beltrami Operators for Shape Analysis and Segmentation". Options for normalization are: None, "area", "index", "areaindex". Normalization by area uses the area of the 2D structure as...


Soichi Hayashi
Service that does nothing (exist to do inter-resource transfer)

BIDS Tracula

Kate Alpert
BIDS app for FS Tracula for BrainLife

multi-LAP with trk

Giulia Berto
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).

Compute Volume of Binary Nifti images

Soichi Hayashi & Lindsey Kitchell
computes the volume of binary nifti images

LAP single example with LiFE

Giulia Berto & Brad Caron
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm with a single example. The user can specify up to eight tracts of interest, otherwise all the tracts of the given segmentation are considered as input.

Bias Field Correction (dwi)

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

Deterministic Tracking

Soichi Hayashi, Serge Koudoro & Aman Arya
Deterministic tracking using a peaks and metrics (PAM) (dipy_track_det)

Quantitative Statistics of Classified Fiber Tracts

Soichi Hayashi, Lindsey Kitchell & Daniel Bullock
This will give you the fiber count, mean length, standard deviation of length, total length, and volume of each fiber tract classified by AFQ or WMA.

Resample tck

Giulia Berto
Code to resample a tck file with a given step size.

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.

Registration Year

  • 2018
  • 2019

Resource Types

  • Software

Data Centers

  • Brainlife Production