brainlife.io

Repositories

• app-tractanalysisprofiles

  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 …

  analysis
  MATLAB MIT 2 1 2 0 Updated Jun 20, 2020

• app-mrtrix3-act

  Runs mrtrix3 ACT (Anatomically Constrained Tractography) using either single- or multi-shell diffusion-weighted MRI data.

  tracking tractography
  Shell 4 0 4 0 Updated Jun 8, 2020

• app-mrtrix3-preproc

  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. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.

  mri diffusion-mri tractography
  Shell 0 0 9 0 Updated Jun 3, 2020

• app-noddi-amico

  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 an optional brainmask of…

  postprocessing
  Shell 1 1 3 0 Updated May 30, 2020

• app-roi2roitracking

  This app will perform ensemble tracking between 2 or more cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. The app will automatically generate ROI niftis in diffusion space for tracking based on inputted ROI numbers. Inputs include: parcellation (freesurfer; atlas optional), dt6 from dtiinit, an…

  tracking
  Shell 3 0 4 0 Updated May 22, 2020

• app-roiGenerator

  Generate a parcellation volume (and roi nifti files split into each label) for specific ROIs, or every ROI, for a parcellation from freesurfer output and/or input parcellation volume. This App can also inflate input parcellation volume toward non-white matter voxels.
  Shell 0 0 1 0 Updated May 21, 2020

• app-hcp-acpc-alignment

  This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.

  anatomy-preprocessing
  Shell 2 1 1 0 Updated May 19, 2020

• docker-fsl

  FSL docker container for Brainlife use
  Dockerfile 4 2 0 0 Updated May 19, 2020

• app-epi-t1-registration

  Preprocess a Diffusion weighted MRI image and aligne it to a T1 image. This App will also: (A) Fit a diffusion tensor model to the DWI data, (B) ... and (C) Create a dt6.mat compatibe with AFQ and VISTA SOFT. INPUTS: DWI data and a T1 image. OUTPUTS dt6.mat, and dt6.json, in addition to processed DWI files.

  diffusion-preprocessing
  Shell 0 1 1 0 Updated May 18, 2020

• app-FSLBET

  Brain Extraction via FSL's BET command

  anatomy-preprocessing
  Shell 0 0 2 0 Updated Apr 22, 2020

• docker-freesurfer

  Docker container for freesurfer
  Dockerfile 0 0 0 0 Updated Apr 13, 2020

• ui-mrview

  MRView / noVNC docker container used by brain-life UI
  Shell 0 0 0 0 Updated Apr 8, 2020

• encode

  Method for encoding brain connectomes in multidimensional arrays (tensors).

  life matlab multidimensional-arrays brain diffusion-mri tractography mba
  MATLAB 23 22 2 0 Updated Mar 9, 2020

• app-ensembletracking

  This App creates a large set of candidate streamlines using an ensemble of algorithms and parameter values. All outputs will be then combined into a single track.tck output.

  tracking
  Shell 1 0 6 0 Updated Mar 1, 2020

• ui-tractview

  HTML5 Tract Viewer - used to visualize output from AFQ
  JavaScript MIT 1 2 2 0 Updated Feb 25, 2020

• app-testflip

  This app will quickly check the dwi image to see if any bvecs directions needs to be flipped. The algorithm finds bvecs that are pointing toward certain direction and find the volume slice within 4D DWI data and see how many image slices indeed seems to contain features that are orthogonal to the bvecs directions. Inconclusive output from this A…

  qa
  Python 0 0 2 0 Updated Feb 21, 2020

• docker-mcr

  MCR (Matlab Compiled Runtime) Docker Container
  Dockerfile 1 6 1 0 Updated Nov 16, 2019

• app-deface

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

  anatomy-preprocessing
  Shell 0 0 1 0 Updated Oct 2, 2019

• app-checkOrientation

  This application checks and reports the orientation (neurological or radiological) of a nifti file.

  qa
  Shell 0 0 0 0 Updated Oct 1, 2019

• ui-mricrogl

  MRIcroGL Viewer for Brainlife
  Shell 0 0 0 0 Updated Jul 10, 2019

• ui-lifeview
  JavaScript 1 0 2 1 Updated Jul 3, 2019

• app-dipy-workflows

  Brainlife wrapper app for Dipy workflows.

  dipy
  Shell 6 0 5 0 Updated May 31, 2019

• mba

  Forked from francopestilli/mba

  Matlab Brain Anatomy. This is a set of routines for displaying and manipulating brain anatomy using MatLab.
  MATLAB BSD-3-Clause 10 0 0 0 Updated May 21, 2019

• docker-pythonvtk

  docker container for python and vtk
  Dockerfile 0 1 0 0 Updated Mar 20, 2019

• ui-volumeviewer

  Brain-Life instance of https://brainbrowser.cbrain.mcgill.ca/
  JavaScript 1 0 1 0 Updated Mar 18, 2019

• app-vistasoft-registration

  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.

  diffusion-preprocessing
  Shell 0 0 1 0 Updated Jan 29, 2019

• app-dt6tonifti

  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.

  convert
  Shell 0 0 0 0 Updated Jan 29, 2019

• vistasoft

  Forked from vistalab/vistasoft

  DEPRECATED: brain-life no longer uses this - we use vistalab/vistasoft
  MATLAB 130 0 0 3 Updated Dec 10, 2018

• ui-fibernavigator

  Docker container for FiberNavigator for Brainlife.io

  neuroscience mri brain diffusion-mri connectome tractography white-matter
  Shell MIT 0 0 0 0 Updated Nov 24, 2018

• o3d-code

  Open Derivatives Diffusion Data scripts used to generate and organize the data
  Python 0 1 7 0 Updated Nov 22, 2018