Repositories list

• ezbids

  Public
  A web service for semi-automated conversion of raw imaging data to BIDS

  webdicominteroperability+ 7mrineuroimagingbidsniftibrain-imagingdata-curationbids-converter

  Vue

  •

  MIT License

  •13•26•10•5•Updated Nov 22, 2024Nov 22, 2024

• app-visual-white-matter

  Public
  Shell

  •2•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• app-hcp-acpc-alignment

  Public
  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

  •

  MIT License

  •4•5•3•1•Updated Nov 11, 2024Nov 11, 2024

• docs

  Public
  Brainlife.io Documentation

  documentationneuroscienceeducational+ 2neuroimagingbrainlife

  HTML

  •26•10•13•2•Updated Nov 6, 2024Nov 6, 2024

• validator-fmap

  Public
  fieldmap datatype validator

  Python

  •1•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• app-qsiprep

  Public
  Preprocessing of diffusion MRI data. It includes automatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, coregister and resample your scans, producing visual reports and QC metrics.

  pipelinepreprocessing

  Python

  •

  MIT License

  •5•2•1•1•Updated Oct 21, 2024Oct 21, 2024

• ui-niivue

  Public
  HTML

  •0•0•1•0•Updated Sep 13, 2024Sep 13, 2024

• amaretti

  Public
  Lightweight task orchestration service for ABCD-specification compatible apps.

  JavaScript

  •

  MIT License

  •4•5•18•10•Updated Sep 1, 2024Sep 1, 2024

• warehouse

  Public
  Service that allows data warehousing and workfow orchestration

  CSS

  •

  MIT License

  •11•12•0•24•Updated Jul 29, 2024Jul 29, 2024

• app-fsl-anat

  Public
  Shell

  •0•0•0•0•Updated Jul 25, 2024Jul 25, 2024

• app-stage

  Public
  App used to stage datasets from archive

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• ga-launcher

  Public
  Group Analysis container Launcher (experimental)

  Shell

  •2•0•1•0•Updated Jul 15, 2024Jul 15, 2024

• pybrainlife

  Public
  Library to access brainlife.io data objects and jupyter notebooks

  python3jupyterlabjupyter-notebooks+ 1brainlifeio

  Python

  •0•2•0•1•Updated Jul 9, 2024Jul 9, 2024

• app-predict-ppcs

  Public
  App to predict Persisting Post Concussion Symptoms

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 29, 2024Jun 29, 2024

• auth

  Public
  Simple, generic authentication service API and UI that issues JWT token

  authenticationjwt

  JavaScript

  •

  MIT License

  •2•0•13•4•Updated Jun 10, 2024Jun 10, 2024

• app-synthstrip

  Public
  Shell

  •0•0•0•0•Updated May 10, 2024May 10, 2024

• app-mriqc

  Public
  Runs MRIQC pipeline (http://mriqc.readthedocs.io/en/stable/reports/smri.html) from Poldrack Lab on selected T1 anatomy.

  qa

  Shell

  •1•0•0•0•Updated May 10, 2024May 10, 2024

• validator-neuro-mask

  Public
  Shell

  •0•0•0•0•Updated May 8, 2024May 8, 2024

• app-fmriprep

  Public
  fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

  fmripreprocessing

  Shell

  •

  MIT License

  •9•2•9•2•Updated Apr 26, 2024Apr 26, 2024

• abcd-spec

  Public
  Application for Big Computational Data Specification (v1.1). This specification provide information on how to write an Application that can run on the open platform

  specificationcloud-computingbrain+ 3biomedical-image-processinghcpcyberinfrastructure

  Python

  •

  MIT License

  •6•8•5•1•Updated Apr 18, 2024Apr 18, 2024

• app-benson14-retinotopy

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

  Shell

  •

  MIT License

  •5•0•0•0•Updated Feb 29, 2024Feb 29, 2024

• app-detect-alpha-peak

  Public
  Detect individual alpha peak in MEG/EEG signals

  meeg

  Python

  •

  MIT License

  •2•0•0•1•Updated Feb 8, 2024Feb 8, 2024

• app-average-tractmasks

  Public
  Shell

  •

  MIT License

  •0•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• app-tractanalysisprofiles

  Public
  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 License

  •4•1•5•0•Updated Feb 1, 2024Feb 1, 2024

• app-clean-parcellation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

• app-cortex-tissue-mapping

  Public
  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.

  postprocessing

  Shell

  •

  MIT License

  •1•1•2•1•Updated Jan 25, 2024Jan 25, 2024

• sample-notebook-for-teaching

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

• bl-app-audit

  Public
  Python

  •1•0•0•0•Updated Jan 25, 2024Jan 25, 2024

• dockerfiles

  Public
  repository to store various dockerfiles used to build docker containers that are used across multiple brainlife apps

  Dockerfile

  •1•2•1•0•Updated Jan 25, 2024Jan 25, 2024

• app-tractDensityMasks

  Public
  This app creates a streamline density mask (NIfTI format) for each structure labeled in a classification structure. This provides information about the volumetric density of streamline models of tracts.

  MATLAB

  •

  MIT License

  •0•0•0•0•Updated Jan 23, 2024Jan 23, 2024