BRANT: A Versatile and Extendable Resting-State fMRI Toolkit

Frontiers in Neuroinformatics
Kaibin XuTianzi Jiang

Abstract

Data processing toolboxes for resting-state functional MRI (rs-fMRI) have provided us with a variety of functions and user friendly graphic user interfaces (GUIs). However, many toolboxes only cover a certain range of functions, and use exclusively designed GUIs. To facilitate data processing and alleviate the burden of manually drawing GUIs, we have developed a versatile and extendable MATLAB-based toolbox, BRANT (BRAinNetome fmri Toolkit), with a wide range of rs-fMRI data processing functions and code-generated GUIs. During the implementation, we have also empowered the toolbox with parallel computing techniques, efficient file handling methods for compressed file format, and one-line scripting. In BRANT, users can find rs-fMRI batch processing functions for preprocessing, brain spontaneous activity analysis, functional connectivity analysis, complex network analysis, statistical analysis, and results visualization, while developers can quickly publish scripts with code-generated GUIs.

References

Dec 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·S OgawaD W Tank
Oct 1, 1995·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·B BiswalJ S Hyde
Mar 1, 1996·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·K J FristonR Turner
Jun 1, 1996·Computers and Biomedical Research, an International Journal·R W Cox
Apr 6, 1999·Archives of Neurology·R C PetersenE Kokmen
Aug 28, 2001·Journal of the American Medical Informatics Association : JAMIA·D C Van EssenC H Anderson
Sep 25, 2001·Behavioural Neurology·Chris Rorden, Matthew Brett
Dec 26, 2001·Archives of Neurology·R C PetersenB Winblad
May 29, 2002·NeuroImage·Nicole A LazarWilliam F Eddy
Apr 15, 2004·Human Brain Mapping·Tianzi JiangXuchu Weng
Apr 28, 2004·NeuroImage·Yufeng ZangLixia Tian
Oct 27, 2004·NeuroImage·Stephen M SmithPaul M Matthews
Apr 6, 2005·NeuroImage·Thomas NicholsJean-Baptiste Poline
Jun 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Michael D FoxMarcus E Raichle
Jul 24, 2008·Human Brain Mapping·Tao WuPiu Chan
Jan 27, 2009·NeuroImage·Gholamreza Salimi-KhorshidiThomas E Nichols
Apr 3, 2009·Journal of Neurophysiology·Michael D FoxMarcus E Raichle
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Oct 13, 2009·NeuroImage·Mikail Rubinov, Olaf Sporns
Oct 27, 2009·Schizophrenia Research·Matthew J HoptmanMichael P Milham
May 12, 2010·Proceedings of the National Academy of Sciences of the United States of America·Dardo Tomasi, Nora D Volkow
Jul 6, 2010·NeuroImage·Andrew ZaleskyEdward T Bullmore
Nov 12, 2010·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Xi-Nian ZuoMichael P Milham
Jun 10, 2011·Journal of Neurophysiology·B T Thomas YeoRandy L Buckner
Aug 4, 2011·NeuroImage·Koene R A Van DijkRandy L Buckner
Sep 6, 2011·NeuroImage·Robert W Cox
Oct 8, 2011·NeuroImage·Mark JenkinsonStephen M Smith
Oct 26, 2011·NeuroImage·John Ashburner
Dec 17, 2011·Science·David N ReshefPardis C Sabeti
May 31, 2012·Brain Connectivity·Susan Whitfield-Gabrieli, Alfonso Nieto-Castanon
May 15, 2013·NeuroImage·Matthew F GlasserUNKNOWN WU-Minn HCP Consortium
May 28, 2013·NeuroImage·Daniel S MarcusUNKNOWN WU-Minn HCP Consortium
Sep 3, 2013·NeuroImage·Jonathan D PowerSteven E Petersen

❮ Previous
Next ❯

Citations

Jan 30, 2020·Human Brain Mapping·Thomas LiebeMartin Walter
Mar 13, 2020·Human Brain Mapping·Zhen ZhouDinggang Shen
Aug 14, 2019·Journal of Alzheimer's Disease : JAD·Wenhao ZhuWei Wang

❮ Previous
Next ❯

Methods Mentioned

BETA
FCS

Software Mentioned

Caret
Sun Grid Engine
GRaph thEoreTical Network Analysis ( GRETNA )
Matlab
Sun Grid Engine ( SGE )
Network Based Statistic ( NBS
DiffusionKit
ReHo
IBMA
fMRI

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.