207 Works

DP Profile with DWI

Soichi Hayashi & Cesar F. Caiafa
Generate FA profiles

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.

Test Gradient Flip for dtiInit processing

Soichi Hayashi & Lindsey Kitchell
This application will provide a recommendation on which axis you should flip the bvecs of your data, if it is necessary. It will perform fiber tracking using 4 different gradient flip options (no flip, x flip, y flip, and z flip) and report the most likely flip needed for your data. The flip recommendation is made based on the flip direction with the highest number of long fibers.

Plot tract measures

Giulia Berto
Compute and plot total number of fibers, total number of nodes and average length of some tracts.

Compute Volume of Binary Nifti images

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

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).

Binary Tract Masks

Soichi Hayashi & Lindsey Kitchell
app to generate binary masks of the segmented fiber tracts

multi-LAP with trk

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

Freesurfer Group Analysis

Soichi Hayashi
Do some basic group analysis on freesurfer outputs

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

wmaSeg - Giulia's patch

Giulia Berto
Classifies streamlines into known anatomical tracts.

Multi-Atlas Transfer Tool

Soichi Hayashi, Josh Faskowitz, Franco Pestilli, Brent McPherson & Brad Caron
brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implemenation of maTT2, which uses the gcs files trained on the mindboggle-101 data. The GCS files are automatically pulled from the maTT fishare directory if not present locally. Inputs include: freesurfer, t1, atlas. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). These outputs are in the space of the T1w that was submitted to FreeSurfer's...

Align DWI to Dtiinit

Soichi Hayashi & Brad Caron
This app will align DWI data to a DTIINIT DWI dataset in order to fit models that require multi-shell data to tracking

Convert wmc-deprecated to wmc

Giulia Berto
App to convert the old wmc-deprecated datatype to the new wmc datatype

FSL Top-up & Eddy

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

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.

FSL BET Brain Extraction (T2)

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

Noddi Amico

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...

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...

ANTs tractogram registration in MNI space

Giulia Berto
ANTs transformation based on T1 and tractogram registration in MNI space

Freesurfer Deface

Soichi Hayashi
Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca

Convert tck to trk in DWI space

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

Registration Year

  • 2018
  • 2019

Resource Types

  • Software

Data Centers

  • Brainlife Production