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BRAPH: A graph theory software for the analysis of brain connectivity

Mijalkov, Mite ; Kakaei, Ehsan ; Pereira, Joana B ; Westman, Eric ; Volpe, Giovanni Hayasaka, Satoru

PloS one, 2017-08, Vol.12 (8), p.e0178798-e0178798 [Peer Reviewed Journal]

United States: Public Library of Science

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Title:
BRAPH: A graph theory software for the analysis of brain connectivity
Author: Mijalkov, Mite ; Kakaei, Ehsan ; Pereira, Joana B ; Westman, Eric ; Volpe, Giovanni
Hayasaka, Satoru
Subjects: Aged ; Aged, 80 and over ; Algorithms ; Alzheimer Disease - diagnostic imaging ; Alzheimer's disease ; ALZHEIMERS-DISEASE ; Amnesia - diagnostic imaging ; Biology and Life Sciences ; Brain ; Brain - physiology ; Brain architecture ; Brain mapping ; Brain research ; Case-Control Studies ; Cluster Analysis ; Cognitive ability ; Cognitive Dysfunction - diagnostic imaging ; Cohort Studies ; Computer and Information Sciences ; Computer architecture ; Computer programs ; Connectivity analysis ; Connectome - methods ; Customization ; EEG ; Electroencephalography ; Engineering and Technology ; Female ; Freeware ; FUNCTIONAL CONNECTIVITY ; Functional magnetic resonance imaging ; Graph theory ; Graphical representations ; Group dynamics ; HUMAN CONNECTOME ; Humans ; Image Processing, Computer-Assisted - methods ; Impairment ; Integrated software ; Magnetic resonance ; Magnetic Resonance Imaging ; Male ; Matrices (mathematics) ; Medical imaging ; Medicin och hälsovetenskap ; Medicine and Health Sciences ; MILD COGNITIVE IMPAIRMENT ; Nanotechnology ; Nerve Net - physiopathology ; Network hubs ; Network topologies ; NETWORKS ; Neural networks ; Neural Pathways - physiopathology ; Neurobiology ; Neuroimaging ; Neurosciences ; Neurovetenskaper ; NMR ; Nodes ; Nuclear magnetic resonance ; Object oriented programming ; Open source software ; Parkinson Disease - diagnostic imaging ; Parkinson's disease ; PARKINSONS-DISEASE ; Patients ; Permutations ; Physical Sciences ; Physics ; Positron emission ; Positron emission tomography ; Research and Analysis Methods ; SCHIZOPHRENIA ; SMALL-WORLD ; Society ; Software ; Software packages ; Structure-function relationships ; Studies ; TIME-VARYING CONNECTIVITY ; Tomography ; TOOLBOX ; TOPOLOGY
Is Part Of: PloS one, 2017-08, Vol.12 (8), p.e0178798-e0178798
Notes: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Conceptualization: JBP EW GV.Data curation: MM EK JBP.Formal analysis: MM EK JBP.Funding acquisition: JBP EW GV.Investigation: MM EK JBP EW GV.Methodology: MM EK JBP EW GV.Project administration: GV.Resources: JBP EW.Software: MM EK GV.Supervision: JBP EW GV.Validation: MM EK JBP EW GV.Visualization: MM EK JBP GV.Writing – original draft: MM EK JBP.Writing – review & editing: MM EK JBP EW GV.
Competing Interests: While commercial funding was obtained by the ADNI and PPMI initiatives, the authors have not directly received commercial funding. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
Description: The brain is a large-scale complex network whose workings rely on the interaction between its various regions. In the past few years, the organization of the human brain network has been studied extensively using concepts from graph theory, where the brain is represented as a set of nodes connected by edges. This representation of the brain as a connectome can be used to assess important measures that reflect its topological architecture. We have developed a freeware MatLab-based software (BRAPH-BRain Analysis using graPH theory) for connectivity analysis of brain networks derived from structural magnetic resonance imaging (MRI), functional MRI (fMRI), positron emission tomography (PET) and electroencephalogram (EEG) data. BRAPH allows building connectivity matrices, calculating global and local network measures, performing non-parametric permutations for group comparisons, assessing the modules in the network, and comparing the results to random networks. By contrast to other toolboxes, it allows performing longitudinal comparisons of the same patients across different points in time. Furthermore, even though a user-friendly interface is provided, the architecture of the program is modular (object-oriented) so that it can be easily expanded and customized. To demonstrate the abilities of BRAPH, we performed structural and functional graph theory analyses in two separate studies. In the first study, using MRI data, we assessed the differences in global and nodal network topology in healthy controls, patients with amnestic mild cognitive impairment, and patients with Alzheimer's disease. In the second study, using resting-state fMRI data, we compared healthy controls and Parkinson's patients with mild cognitive impairment.
Publisher: United States: Public Library of Science
Language: English

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BRAPH: A graph theory software for the analysis of brain connectivity

Mijalkov, Mite ; Kakaei, Ehsan ; Pereira, Joana B ; Westman, Eric ; Volpe, Giovanni Hayasaka, Satoru

United States: Public Library of Science

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