List of functional connectivity software

Functional connectivity software is used to study functional properties of the connectome using functional Magnetic Resonance Imaging (fMRI) data in the resting state and during tasks. To access many of these software applications visit the NIH funded Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) site.

NameDescriptionProgramming languageIs part of / requiresDeveloper/Organization
Brain Connectivity Toolbox[1]Graph-theoretical analyses of functional connectivityMatlabDepartment of Psychological and Brain Sciences, Indiana University
Brain Modulyzer [2] Explore Hierarchical Processes of the functional brain networks PythonU.S. Dept. of Energy, Lawrence Berkeley National Laboratory
BrainNet viewer[3]Brain network visualization toolMatlabNational Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University
Brainwaver[4]Brain connectivity extraction and analysisRwaveslimCentre National de la Recherche Scientifique, GIPSA-lab, University of Cambridge
C-PAC[5]Functional connectivity analysis pipelinePythonChild Mind Institute; Nathan Kline Institute; NYU Langone Medical Center
CONN[6]Functional connectivity analysis and display toolMatlabSPMMcGovern Institute for Brain Research, Massachusetts Institute of Technology: MIT
Connectome workbenchVisualization and discovery toolPythonChild Mind Institute, Nathan Kline Institute, NYU Langone Medical Center
cPPI[7]Task-related functional connectivity analysisMatlabSPMMonash Clinical and Imaging Neuroscience
DCM[8]Dynamic Causal Modelling analysisMatlabSPMWellcome Trust Centre for Neuroimaging, University College London
FATCAT[9]Functional and tractographic connectivity analysisCAFNIScientific and Statistical Computing Core, National Institute of Mental Health: NIMH
FSFC[10]Seed-based functional connectivity analysisShellFreeSurferMartinos Center for Biomedical Imaging
Fubraconnex[11]Tool for visual analysis of functional connectivityCDelft University of Technology
GIFT[12]Independent component analysisMatlabMedical Image Analysis Lab, The Mind Research Network
gPPI[13]Task-related functional connectivity analysisMatlabSPMUniversity of Wisconsin Madison
Graph Theoretic GLM Toolbox[14] Graph theory analysis and fMRI preprocessing pipeline MatlabBoston University School of Medicine, VA Boston Healthcare System
Graphvar[15]Graph-theoretical analysis toolMatlabDivision of Mind and Brain Research, Charité Universitätsmedizin
MELODIC[16]Independent component analysisCFSLFunctional Magnetic Resonance Imaging of the Brain Analysis Group, Oxford University
NIAK[17]Neuroimaging analysis libraryMatlab, OctaveResearch Centre of the Montreal Geriatric Institute, University of Montreal
nilearn[18]Machine learning for Neuro-Imaging in PythonPythonINRIA Parietal Project Team, Neurospin, CEA Institute
REST[19]Resting-state functional connectivity analysis toolMatlabState Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University

See also

References

  1. ↑ Rubinov, M.; Sporns, O. (2010). "Complex network measures of brain connectivity: uses and interpretations". NeuroImage. 52: 1059–1069. doi:10.1016/j.neuroimage.2009.10.003.
  2. ↑ Murugesan, S.; Bouchard, K.; Brown, J. A.; Hamann, B.; Seeley, W. W.; Trujillo, A.; Weber, G. H. (2016-01-01). "Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity". IEEE/ACM Transactions on Computational Biology and Bioinformatics. PP (99): 1–1. doi:10.1109/TCBB.2016.2564970. ISSN 1545-5963.
  3. ↑ Xia, M.; Wang, J.; He, Y. (2013). "BrainNet Viewer: a network visualization tool for human brain connectomics". PLoS ONE. 8: e68910. doi:10.1371/journal.pone.0068910.
  4. ↑ Achard, S.; Salvador, R.; Whitcher, B.; Suckling, J.; Bullmore, Ed (2006). "Brainwaver: Basic wavelet analysis of multivariate time series with a visualisation and parametrisation using graph theory". J. Neurosci. 26 (1): 63-72. doi:10.1523/JNEUROSCI.3874-05.2006.
  5. ↑ Di Martino, A.; et al. (2014). "The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecturein autism". Mol. Psychiatry. 19: 659–667. doi:10.1038/mp.2013.78.
  6. ↑ Whitfield-Gabrieli, S.; Nieto-Castanon, A. (2012). "Conn: a functional connectivity toolbox for correlated and anticorrelated brainnetworks". Brain Connect. 2: 125–141. doi:10.1089/brain.2012.0073.
  7. ↑ Fornito, A.; Harrison, B. J.; Zalesky, A.; Simons, J.S. (2012). "Competitive and cooperative dynamics of large-scale brain functional networks supporting recollection". PNAS. 109 (31): 12788–12793. doi:10.1073/pnas.1204185109. PMC 3412011. PMID 22807481.
  8. ↑ Friston, K. J.; Kahan, J.; Biswal, B.; Razi, A. (2014). "A DCM for resting state fMRI". NeuroImage. 94: 396–407. doi:10.1016/j.neuroimage.2013.12.009.
  9. ↑ Taylor, P. A.; Saad, Z. S. (2013). "FATCAT: (an efficient) Functional and Tractographic Connectivity Analysis Toolbox". Brain Connect. 3: 523–535. doi:10.1089/brain.2013.0154. PMC 3796333.
  10. ↑ Fischl, B. FreeSurfer (2012). "FreeSurfer". NeuroImage. 62: 774–781. doi:10.1016/j.neuroimage.2012.01.021. PMC 3685476.
  11. ↑ van Dixhoorn, A.F., Vissers, B., Ferrarini, L., Milles, J., and Botha, C.P. (2010). Visual analysis of integrated resting state functional brain connectivity and anatomy, Eurographics Workshop on Visual Computing for Biology and Medicine
  12. ↑ Calhoun, V. D., Adali, T., Pearlson, G. D. & Pekar, J. J. (2001). A method for making group inferences from functional MRI data using independent component analysis. Hum. Brain Mapp. 14, 140–151
  13. ↑ McLaren, D.G., Ries, M.L., Xu, G., Johnson, S.C. (2012). A generalized form of context-dependent psychophysiological interactions (gPPI): A comparison to standard approaches, NeuroImage, 61(4), 1277-1286
  14. ↑ Spielberg, Jeffrey M.; McGlinchey, Regina E.; Milberg, William P.; Salat, David H. "Brain Network Disturbance Related to Posttraumatic Stress and Traumatic Brain Injury in Veterans". Biological Psychiatry. 78 (3): 210–216. doi:10.1016/j.biopsych.2015.02.013. PMID 25818631.
  15. ↑ Kruschwitz, J. D.; List, D.; Waller, L.; Rubinov, M.; Walter, H. (2015). "GraphVar: A user-friendly toolbox for comprehensive graph analyses of functional brain connectivity". Journal of Neuroscience Methods. 245: 107–115. doi:10.1016/j.jneumeth.2015.02.021.
  16. ↑ Beckmann, C. F.; DeLuca, M.; Devlin, J. T.; Smith, S. M. (2005). "Investigations into resting-state connectivity using independentcomponent analysis". Philos. Trans. R. Soc. Lond. B Biol. Sci. 360: 1001–1013. doi:10.1098/rstb.2005.1634. PMC 1854918.
  17. ↑ Bellec, P.; et al. (2012). "The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine forscientific workflows". Front. Neuroinformatics. 6: 7. doi:10.3389/fninf.2012.00007.
  18. ↑ Abraham, A., Pedregosa, F., Eickenberg, M., Gervais, P., Mueller, A., Kossaifi, J., ... & Varoquaux, G. (2014). Machine learning for neuroimaging with scikit-learn. Frontiers in neuroinformatics, 8
  19. ↑ Song, X. W.; et al. (2011). "REST: a toolkit for resting-state functional magnetic resonance imaging data processing". PLoS ONE. 6: e25031. doi:10.1371/journal.pone.0025031.
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