Excerpt

hidden	true

Tutorials with the main external toobloxes used at the CENIR.

Filter by label (Content by label)

showSpace	false
cql	label = "kb-how-to-article" and ancestor = currentContent ( ) and type = "page"

Create from Template

blueprintModuleCompleteKey	com.atlassian.confluence.plugins.confluence-knowledge-base:kb-how-to-article-blueprint
contentBlueprintId	6d3de2dd-eb17-4952-839a-c7eac973241c
templateName	6d3de2dd-eb17-4952-839a-c7eac973241c
buttonLabel	Create a toolbox tutorial

Brainstorm

Brainstorm is an open-source analysis software working under MATLAB. It was originally developed in the MEG-EEG center at the Pitié-Salpêtrière hospital by Sylvain Baillet. Brainstorm is nowadays developed at the McGill University in Montréal by a whole team of developers.

FieldTrip

Fieldtrip is an open-source analysis software working under MATLAB. It is developed by Robert Oostenveld and coworkers at the Donders Institute for Brain and Cognition in Nijmegen.

MNE-python

MNE-python is an open-source analysis software working in Python. It was initiated by Alexandre Gramfort and is nowadays developed by an important community.

Strengths: Brainstorm is a complete toolbox that requires no programming skills. Its stable and elegant powerful graphical user interface allows a rapid "point and click" exploration of source reconstruction results. Historically developed for MEG data analysis, it is very well suited for this technology with several "safeguards" that prevent forgetting important steps in the analysis. The data organization is very well structured. Programmers will also enjoy its powerful API, and a growing plugin environment.

Strengths: FieldTrip is a complete toolbox with a minimalist concise data structure and a command line user interface, allowing maximal flexibility. Historically developed for time-frequency analysis, it remains a leader in this domain. It also has a real-time interface for brain computer interface.

Strengths: MNE-Python is a complete toolbox with strong signal processing capabilities. The Python open-source language is widely usedbonds to machine learning via its interface with scikit-learn. A historical connection to the MNE source estimation tools and Freesurfer (MRI segmentation) make it easy to interface with these tools.

Weaknesses: A It is hard to think of any weakness for this amazing toolbox. Perhaps, its strict data organization implies constraints and limited that are great for robustness, provenance tracking and reproducibility, but may limit flexibility for complex/unconventional designs. Time-frequency analysis is limited and data access via user interface can turn out fastidious.

Weaknesses: The command line interface is a no-go for users who are not ready to learn at least rudiments of programming. Rapid data exploration requires a good mastery of the software.

Weaknesses: The user base still has to grow in our community. MATLAB is at present (2018) still a leading comfortable tool in brain imaging sciencesonly limits are your imagination, and your ability to write python code.

Target users:Beginner users All users will find an incredible environment with the most advanced and accessible visualization tools to interact with the data. Users without prior experience with MATLAB will find their way easily through Brainstorm. More advanced users will be satisfied by the export functionalities that also allow flexible export.

Target users: Users with prior experience (and appetite) using MATLAB will enjoy this tool.

Target users: Users with prior programming experience will be most at ease with MNE-python. A good occasion to learn the Python language.

Native BIDS support via import function

BIDS support via external bids-matlab library

BIDS support via external mne-bids library