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This tool is supported wholly or in part by The Human Brain Project.

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Name
BAMM
Byline
University of Cambridge, King's College London and the Wellcome Trust
Description

A complete fMRI analysis package created with batch processing in mind. The software comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution. The software is mostly written in C.

Development of this software is supported as Human Brain Project/Neuroinformatics research funded by the National Institute of Biomedical Imaging and Bioengineering, and the National Institute of Mental Health.

NIfTI-1 support
Creator
Ed Bullmore, Mick Brammer, John Suckling
Contact
Dr Cinly Ooi (co224@cam.ac.uk)
WWW
www-bmu.psychiatry.cam.ac.uk/software/
Availability
Now
How to get
http://www-bmu.psychiatry.cam.ac.uk/software/download
Current version
See website
Current version release date
See website
Open source
Yes
License
Free for academic use.
Available free of charge
Yes
Requirements
Binary distribution:
Solaris and Linux.

To compile it yourself from source:
C and C++. A small, non-critical, subset of code requires Motif Library. Source code is known to compile on Linux (Debian), Solaris 7 and 8, and Mac OS X.
Technical publications
(BAMM is continuously being developed and as such, it is not possible to maintain an up-to-date list here. For a complete and uptodate list, please visit website http://www-bmu.psychiatry.cam.ac.uk/software/publications/ for more detail)

Brammer MJ, Bullmore ET, Simmons A, Williams SCR, Grasby PM, Howard RJ, Woodruff PWR & Rabe-Hesketh S (1997)
Generic brain activation mapping in fMRI: a nonparametric approach.
Magnetic Resonance Imaging; 15, 763-770.

Bullmore ET, Brammer MJ, Rouleau G, Everitt BS, Simmons A, Sharma T, Frangou S, Murray RM & Dunn G (1995)
Computerised brain tissue classification of magnetic resonance images: a new approach to the problem of partial volume artefact.
NeuroImage; 2: 133-147.

Bullmore ET, Rabe-Hesketh S, Morris RG, Williams SCR, Gregory L, Gray JA, Brammer MJ (1996)
Functional magnetic resonance image analysis of a large-scale neurocognitive network.
NeuroImage; 4: 16-33.

Bullmore ET, Brammer MJ, Rabe-Hesketh S, Janot N, Williams SCR, Mellers JDC, David AS, Howard R & Sham P (1996)
Statistical methods of estimation and inference for functional MR image analysis.
Magnetic Resonance in Medicine; 35: 261-277.

Bullmore ET, Brammer MJ, Rabe-Hesketh S, Curtis VA, Morris RG, Williams SCR, Sharma T & McGuire PK (1999)
Methods for diagnosis and treatment of stimulus correlated motion in generic brain activation studies using fMRI.
Human Brain Mapping, 7: 38-48.

Bullmore ET, Suckling J, Overmeyer S, Rabe-Hesketh S, Taylor E & Brammer MJ (1999)
Global, voxel and cluster tests, by theory and permutation, for a difference between two groups of structural MR images of the brain.
IEEE Transactions on Medical Imaging, 18, 32-42.

Bullmore ET, Brammer MJ, Williams SCR, Curtis VA, McGuire PK, Morris RG, Murray RM & Sharma T (1999)
Functional MR imaging of confounded hypofrontality.
Human Brain Mapping, 8 86-91.

Bullmore ET, Horwitz B, Honey GD, Brammer MJ, Williams SCR & Sharma T (2000)
How good is good enough in path analysis of fMRI data?
NeuroImage 11, 289-301.

Bullmore ET & Suckling J (2000)
Functional MRI.
In The New Oxford Textbook of Psychiatry (Ed. M. Gelder, N. C. Andreasen, J. Lopez-Ibor), 1, 218-223; and International Review of Psychiatry 13, 24-33.

Bullmore ET, Suckling J & Brammer MJ (2001)
In praise of tedious permutation. In Spatial Statistics: Methodological aspects and some applications. (Ed. M Moore).
Lecture notes in statistics. New York: Springer.

Bullmore ET, Long C, Suckling J, Fadili J, Calvert GA, Zelaya FO, Carpenter TA & Brammer MJ (2001)
Colored noise and computational inference in neurophysiological (fMRI) time series analysis: Resampling methods in the time and wavelet domains.
Human Brain Mapping, 12, 61-78.

Everitt BS & Bullmore ET (1999)
Mixture model mapping of brain activation in functional magnetic resonance images.
Human Brain Mapping, 7: 1-14.

Fadili J & Bullmore ET (2001)
Wavelet-generalised least squares: a new BLU estimator of regression models with long-memory errors.
NeuroImage.

Fadili J, Brett M & Bullmore ET (2001)
Wavelet methods for characterising mono- and poly-fractal noise structures in shortish time series: An application to functional MRI.
Proceedings ICIP.

Landau S, Wright IC & Bullmore ET (2001)
Tests for a difference in timing of physiological response between two brain regions measured using fMRI.
Applied Statistics, under review.

Rabe-Hesketh S, Bullmore ET & Brammer MJ (1997)
Analysis of functional magnetic resonance images.
Statistical Methods in Medical Research: 6, 215-237.

Suckling J, Sigmundsson T, Greenwood K & Bullmore ET (1999)
A modified fuzzy clustering algorithm for operator independent brain tissue classification of dual echo MR images.
Magnetic Resonance Imaging, 17, 1065-1076.

Suckling J, Brammer MJ, Lingford-Hughes A & Bullmore ET (1999)
Removal of extracortical tissues in dual-echo magnetic resonance images via linear scale space features.
Magnetic Resonance Imaging, 17, 247-256.

Suckling J & Bullmore ET (2000)
Structural MRI.
In The New Oxford Textbook of Psychiatry (Ed. M. Gelder, N. C. Andreasen, J. J. Lopez-Ibor), 1, 212-218.

Wright IC, Sharma T, McGuire PK, Sharma T, Friston KJ, Murray RM & Bullmore ET (1999)
Supraregional brain systems and the neuropathology of schizophrenia.
Cerebral Cortex, 9, 366-378.
Applications publications
(100+ applications papers in total and counting. It is not possible to maintain an up-to-date list here so please refers to the website http://www-bmu.psychiatry.cam.ac.uk/software/publications/usingBAMM/ for a more uptodate listing)
Ng VWK, Bullmore ET, de Zubicaray GI, Cooper A & Williams SCR (2001)
Identifying critical nodes in large-scale cortical networks subserving visuospatial processing: an illustration using fMRI.
Journal of Cognitive Neuroscience, 13 537-545.

Rubia K, Overmeyer S, Russell T, Brammer MJ, Bullmore ET, Sharma T, Simmons A, Williams SCR, Andrew CM & Taylor E (2001)
Mapping motor inhibition: Conjunctive brain activations across different versions of go/no-go and stop tasks.
NeuroImage 13, 239-249.

Toosy AT, Werring DJ, Plant GT, Bullmore ET, Miller DH & Thompson AJ (2001)
Nasotemporal asymmetries of the ocular dominance regions in human visual cortex demonstrated by functional MRI.
NeuroImage 14, 632-641.

Other information
Keywords
ANOVA, functional, HBP supported, registration, resampling, statistical, wavelet
Platforms
Linux, MacOS, UNIX
IATR listing last updated
03 May 2005