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Reference

Applications

Reference

The neuroscience tools available in CHORUS.HIP, grouped by purpose - each group listed alphabetically.

In short

CHORUS.HIP comes with ready-to-use tools grouped by what they're for - signal analysis, imaging and electrode localization, modelling, data preparation, and general computing. You launch them from the App Store inside a session; nothing is installed on your own computer. More can be added on request.

Signal analysis & visualization​

  • AnyWave - open and view data recorded by EEG or MEG acquisition systems.
  • Brainstorm - analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes, multiunit electrophysiology. Used in three of the tutorials.
  • Frites - information-theoretic measures on neurophysiological data, in Python.
  • HiBoP - visualization of intracranial recordings: iEEG, CCEP, and fMRI.
  • Localizer - processes raw brain recordings into frequency responses.
  • MNE-Python - exploring, visualizing and analyzing MEG, EEG, sEEG, ECoG and NIRS data.

Imaging & electrode localization​

  • 3D Slicer - multi-platform package for medical and biomedical imaging research. Used in Place SEEG electrodes with 3D Slicer.
  • CiCLONE - automated SEEG pipeline for image co-registration and electrode localization. See the tutorial.
  • dcm2niix - converts neuroimaging data from DICOM to NIfTI.
  • FreeSurfer - processing, analyzing and visualizing human brain MR images.
  • FSL - analysis tools for FMRI, MRI and DTI brain imaging data.
  • GARDEL - automatic segmentation and labelling of SEEG contacts.
  • IntrAnat - database and visualization software for intracranial EEG data.
  • MRIcroGL - viewing DICOM and NIfTI images.
  • MRtrix3 - diffusion MRI analysis and tractography.
  • NiftyReg - medical image registration.

Modelling & simulation​

Data preparation & standards​

These do not replace de-identification at the source

Defacing and anonymization tools are here so you can check and complete work on data that is already de-identified. Removing direct identifiers remains the contributing institution's job, done before transfer - see Upload iEEG data.

General computing​

  • Jupyter - notebooks for interactive analysis.
  • LibreOffice - documents, spreadsheets and presentations.
  • MATLAB - scripting and numerical computing.
  • RStudio - development environment for R and statistical computing.
  • VS Code - a full code editor.
  • File manager - browsing and organizing files inside your session.
This is a selection, and versions change

The catalogue evolves and new tools can be added on request - ask support@thehip.app. The App Store inside the platform is what shows the versions actually available to you; several tools offer more than one.

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