List of functional connectivity software
Appearance
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.
Name | Description | Programming language | Is part of / requires | Developer/Organization |
---|---|---|---|---|
Brain Connectivity Toolbox[1] | Graph-theoretical analyses of functional connectivity | Matlab | Department of Psychological and Brain Sciences, Indiana University | |
Brain Modulyzer [2] | Explore Hierarchical Processes of the functional brain networks | Python | U.S. Dept. of Energy, Lawrence Berkeley National Laboratory | |
BrainNet viewer[3] | Brain network visualization tool | Matlab | National Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University | |
Brainwaver[4] | Brain connectivity extraction and analysis | R | waveslim | Centre National de la Recherche Scientifique, GIPSA-lab , University of Cambridge |
C-PAC[5] | Functional connectivity analysis pipeline | Python | Child Mind Institute; Nathan Kline Institute; NYU Langone Medical Center | |
CONN[6] | Functional connectivity analysis and display tool | Matlab | SPM | McGovern Institute for Brain Research, Massachusetts Institute of Technology: MIT |
Connectome workbench | Visualization and discovery tool | Python | Child Mind Institute, Nathan Kline Institute, NYU Langone Medical Center | |
cPPI[7] | Task-related functional connectivity analysis | Matlab | SPM | Monash Clinical and Imaging Neuroscience |
DCM[8] | Dynamic Causal Modelling analysis | Matlab | SPM | Wellcome Trust Centre for Neuroimaging, University College London |
FATCAT[9] | Functional and tractographic connectivity analysis | C | AFNI | Scientific and Statistical Computing Core, National Institute of Mental Health: NIMH |
FSFC[10] | Seed-based functional connectivity analysis | Shell | FreeSurfer | Martinos Center for Biomedical Imaging |
Fubraconnex[11] | Tool for visual analysis of functional connectivity | C | Delft University of Technology | |
GIFT[12] | Independent component analysis | Matlab | Medical Image Analysis Lab, The Mind Research Network | |
gPPI[13] | Task-related functional connectivity analysis | Matlab | SPM | University of Wisconsin Madison |
Graph Theoretic GLM Toolbox[14] | Graph theory analysis and fMRI preprocessing pipeline | Matlab | Boston University School of Medicine, VA Boston Healthcare System | |
Graphvar[15] | Graph-theoretical analysis tool | Matlab | Division of Mind and Brain Research, Charité Universitätsmedizin | |
MELODIC[16] | Independent component analysis | C | FSL | Functional Magnetic Resonance Imaging of the Brain Analysis Group, Oxford University |
NIAK[17] | Neuroimaging analysis library | Matlab, Octave | Research Centre of the Montreal Geriatric Institute, University of Montreal | |
nilearn[18] | Machine learning for Neuro-Imaging in Python | Python | INRIA Parietal Project Team, Neurospin, CEA Institute | |
REST[19] | Resting-state functional connectivity analysis tool | Matlab | State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University | |
o8t Labs | Automated functional and structural connectivity pipeline & visualization | Python | Omniscient Neurotechnology |
See also
References
- ^ Rubinov, M.; Sporns, O. (2010). "Complex network measures of brain connectivity: uses and interpretations". NeuroImage. 52 (3): 1059–1069. doi:10.1016/j.neuroimage.2009.10.003. PMID 19819337.
- ^ 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" (PDF). IEEE/ACM Transactions on Computational Biology and Bioinformatics. PP (99): 805–818. doi:10.1109/TCBB.2016.2564970. ISSN 1545-5963. PMC 5585064. PMID 28113724.
- ^ Xia, M.; Wang, J.; He, Y. (2013). "BrainNet Viewer: a network visualization tool for human brain connectomics". PLoS ONE. 8 (7): e68910. doi:10.1371/journal.pone.0068910. PMC 3701683. PMID 23861951.
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: CS1 maint: unflagged free DOI (link) - ^ 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. PMID 16399673.
- ^ 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 (6): 659–667. doi:10.1038/mp.2013.78. PMC 4162310. PMID 23774715.
- ^ Whitfield-Gabrieli, S.; Nieto-Castanon, A. (2012). "Conn: a functional connectivity toolbox for correlated and anticorrelated brainnetworks". Brain Connect. 2 (3): 125–141. doi:10.1089/brain.2012.0073. PMID 22642651.
- ^ 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.
- ^ 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. PMC 4073651. PMID 24345387.
- ^ Taylor, P. A.; Saad, Z. S. (2013). "FATCAT: (an efficient) Functional and Tractographic Connectivity Analysis Toolbox". Brain Connect. 3 (5): 523–535. doi:10.1089/brain.2013.0154. PMC 3796333. PMID 23980912.
- ^ Fischl, B. FreeSurfer (2012). "FreeSurfer". NeuroImage. 62 (2): 774–781. doi:10.1016/j.neuroimage.2012.01.021. PMC 3685476. PMID 22248573.
- ^ 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
- ^ 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
- ^ 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
- ^ Spielberg, Jeffrey M.; McGlinchey, Regina E.; Milberg, William P.; Salat, David H. (2015). "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.
- ^ 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. PMID 25725332.
- ^ 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 (1457): 1001–1013. doi:10.1098/rstb.2005.1634. PMC 1854918. PMID 16087444.
- ^ Bellec, P.; et al. (2012). "The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine forscientific workflows". Front. Neuroinform. 6: 7. doi:10.3389/fninf.2012.00007. PMC 3318188. PMID 22493575.
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: CS1 maint: unflagged free DOI (link) - ^ 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
- ^ Song, X. W.; et al. (2011). "REST: a toolkit for resting-state functional magnetic resonance imaging data processing". PLoS ONE. 6 (9): e25031. doi:10.1371/journal.pone.0025031. PMC 3176805. PMID 21949842.
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: CS1 maint: unflagged free DOI (link)