Cambridge Brain Analysis
Encyclopedia
Cambridge Brain Analysis (CamBA), is a software repository developed at the Brain Mapping Unit, Department of Psychiatry, University of Cambridge
, UK and contains software pipelines for functional magnetic resonance imaging
(fMRI) analysis. It is designed for batch processing
and its main graphical user interface
offers a spreadsheet
-like look-and-feel.
The software is available under the GNU General Public License
and runs under Linux
. Up-to-date information is available at CamBA's project description page at the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).
begin in 1996 at the Institute of Psychiatry
, King's College London
, London
, UK. Professor Ed Bullmore and Professor Mick Brammer wrote a small package of software components
to process functional magnetic resonance imaging
data, which at that time was an emerging technology. In 1999 Dr John Suckling became involved in the first effort to coordinate and organise the software including options for processing structural MRI images and between-subject statistical inference
, based on randomisation methods.
The CamBA initiative began in 2006. Instead of a library of functions, CamBA is better described as a software repository
. It is an Eclipse
RCP
-based application and contains a number of pipelines which are constructed from software modules contributed by a variety of authors using a common ontology
.
of resting state acquisitions and second-level (between-subject) analysis based on randomisation (permutation) methods.
University of Cambridge
The University of Cambridge is a public research university located in Cambridge, United Kingdom. It is the second-oldest university in both the United Kingdom and the English-speaking world , and the seventh-oldest globally...
, UK and contains software pipelines for functional magnetic resonance imaging
Functional magnetic resonance imaging
Functional magnetic resonance imaging or functional MRI is a type of specialized MRI scan used to measure the hemodynamic response related to neural activity in the brain or spinal cord of humans or other animals. It is one of the most recently developed forms of neuroimaging...
(fMRI) analysis. It is designed for batch processing
Batch processing
Batch processing is execution of a series of programs on a computer without manual intervention.Batch jobs are set up so they can be run to completion without manual intervention, so all input data is preselected through scripts or command-line parameters...
and its main graphical user interface
Graphical user interface
In computing, a graphical user interface is a type of user interface that allows users to interact with electronic devices with images rather than text commands. GUIs can be used in computers, hand-held devices such as MP3 players, portable media players or gaming devices, household appliances and...
offers a spreadsheet
Spreadsheet
A spreadsheet is a computer application that simulates a paper accounting worksheet. It displays multiple cells usually in a two-dimensional matrix or grid consisting of rows and columns. Each cell contains alphanumeric text, numeric values or formulas...
-like look-and-feel.
The software is available under the GNU General Public License
GNU General Public License
The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project....
and runs under Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
. Up-to-date information is available at CamBA's project description page at the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).
History
The origins of the CamBA software repositorySoftware repository
A software repository is a storage location from which software packages may be retrieved and installed on a computer.- Discussion :Many software publishers and other organizations maintain servers on the Internet for this purpose, either free of charge or for a subscription fee...
begin in 1996 at the Institute of Psychiatry
Institute of Psychiatry
The Institute of Psychiatry is a research institution dedicated to discovering what causes mental illness and diseases of the brain. In addition, its aim is to help identify new treatments for them and ways to prevent them in the first place...
, King's College London
King's College London
King's College London is a public research university located in London, United Kingdom and a constituent college of the federal University of London. King's has a claim to being the third oldest university in England, having been founded by King George IV and the Duke of Wellington in 1829, and...
, London
London
London is the capital city of :England and the :United Kingdom, the largest metropolitan area in the United Kingdom, and the largest urban zone in the European Union by most measures. Located on the River Thames, London has been a major settlement for two millennia, its history going back to its...
, UK. Professor Ed Bullmore and Professor Mick Brammer wrote a small package of software components
Component-based software engineering
Component-based software engineering is a branch of software engineering that emphasizes the separation of concerns in respect of the wide-ranging functionality available throughout a given software system...
to process functional magnetic resonance imaging
Functional magnetic resonance imaging
Functional magnetic resonance imaging or functional MRI is a type of specialized MRI scan used to measure the hemodynamic response related to neural activity in the brain or spinal cord of humans or other animals. It is one of the most recently developed forms of neuroimaging...
data, which at that time was an emerging technology. In 1999 Dr John Suckling became involved in the first effort to coordinate and organise the software including options for processing structural MRI images and between-subject statistical inference
Statistical inference
In statistics, statistical inference is the process of drawing conclusions from data that are subject to random variation, for example, observational errors or sampling variation...
, based on randomisation methods.
The CamBA initiative began in 2006. Instead of a library of functions, CamBA is better described as a software repository
Software repository
A software repository is a storage location from which software packages may be retrieved and installed on a computer.- Discussion :Many software publishers and other organizations maintain servers on the Internet for this purpose, either free of charge or for a subscription fee...
. It is an Eclipse
Eclipse (software)
Eclipse is a multi-language software development environment comprising an integrated development environment and an extensible plug-in system...
RCP
Rich Client Platform
A rich client platform is software consisting of the following components:* A core , lifecycle manager* A standard bundling framework* A portable widget toolkit* File buffers, text handling, text editors...
-based application and contains a number of pipelines which are constructed from software modules contributed by a variety of authors using a common ontology
Ontology
Ontology is the philosophical study of the nature of being, existence or reality as such, as well as the basic categories of being and their relations...
.
Pipelines
Currently pipelines are available for analysis of fMRI activation paradigms, spectral analysisSpectrum analysis
Spectrum, also known as emission spectrochemical analysis, is the original scientific method of charting and analyzing the chemical properties of matter and gases by looking at the bands in their optical spectrum...
of resting state acquisitions and second-level (between-subject) analysis based on randomisation (permutation) methods.
Current and past contributors
- Dr Sanja Abbott
- Dr Sophie Achard
- Mr John Aspden
- Dr Anna Barnes
- Prof Mick Brammer
- Prof Ed Bullmore
- Dr Jalal Fadili
- Dr Vincent Giampietro
- Dr Manfred Kitzbichler
- Dr Chris Long
- Dr Vochita Maxim
- Dr Cinly Ooi
- Dr Levent Sendur
- Dr John Suckling
- Dr Alle Meije Wink
See also
- functional magnetic resonance imagingFunctional magnetic resonance imagingFunctional magnetic resonance imaging or functional MRI is a type of specialized MRI scan used to measure the hemodynamic response related to neural activity in the brain or spinal cord of humans or other animals. It is one of the most recently developed forms of neuroimaging...
- functional neuroimagingFunctional neuroimagingFunctional neuroimaging is the use of neuroimaging technology to measure an aspect of brain function, often with a view to understanding the relationship between activity in certain brain areas and specific mental functions...
- neuroimagingNeuroimagingNeuroimaging includes the use of various techniques to either directly or indirectly image the structure, function/pharmacology of the brain...
- AFNI
- FreeSurferFreeSurferFreeSurfer is an MRI brain imaging software package developed by the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital. It is an important tool in functional brain mapping and facilitates the visualization of the functional regions of the highly-folded cerebral...
- FSLFMRIB Software LibraryThe FMRIB Software Library is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data....
- SPMStatistical parametric mappingStatistical parametric mapping or SPM is a statistical technique created by Karl Friston for examining differences in brain activity recorded during functional neuroimaging experiments using neuroimaging technologies such as fMRI or PET...
External links
- List of academic publications on CamBA
- List of academic publications that uses CamBA in their data analysis
- Brain Mapping Unit (BMU), University of CambridgeUniversity of CambridgeThe University of Cambridge is a public research university located in Cambridge, United Kingdom. It is the second-oldest university in both the United Kingdom and the English-speaking world , and the seventh-oldest globally...
- Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), CamBA resource page