GLMdenoise specifications

Information


Unique identifier OMICS_17596
Name GLMdenoise
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A design matrix and fMRI time-series.
Output data An estimate of the hemodynamic response function and BOLD response amplitudes.
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Kendrick Kay <>
  • person_outline Ian Charest <>

Publications for GLMdenoise

GLMdenoise in publications

 (8)
PMCID: 5846788
PMID: 29529085
DOI: 10.1371/journal.pone.0193107

[…] frequency signals. in order to increase the signal-to-noise ratio, we developed a denoising technique that helps reveal the broadband signal of interest. a denoising algorithm developed for fmri (‘glmdenoise’; []) was adapted for meg to project out noise from the data for each epoch in each sensor. the logic behind the algorithm is that many sources of noise are global, and therefore spread […]

PMCID: 5469028
PMID: 28612049
DOI: 10.1523/ENEURO.0159-17.2017

[…] as a second parametric modulator, choice ll was entered. parametric modulators were also convolved with the hrf. button pressed were modeled separately. we built nuisance regressors using the glmdenoise toolbox (). glmdenoise extracts principal components from voxels that are unrelated to the task (i.e., voxels in which the r 2 is smaller than 0%). the signal in these components […]

PMCID: 5234071
PMID: 28072399
DOI: 10.1038/ncomms13995

[…] correction) were used to minimize effects of head motion. last, five principal component analysis (pca)-based noise regressors were used to account for other noise sources (a method similar to glmdenoise). pca-based regressors were defined by: (1) choosing a ‘noise pool' of voxels with <1% of variance explained by the task regressors; (2) running pca on time series from these voxels; […]

PMCID: 5358981
PMID: 28226243
DOI: 10.7554/eLife.22341.013

[…] performed directly at the vertices of the subject’s cortical surface, thereby avoiding unnecessary interpolation and improving spatial resolution ()., the pre-processed fmri data were analyzed using glmdenoise () (http://kendrickkay.net/glmdenoise/), a data-driven denoising method that derives estimates of correlated noise from the data and incorporates these estimates as nuisance regressors […]

PMCID: 5102698
PMID: 27417345
DOI: 10.1016/j.neuroimage.2016.07.022

[…] a conventional task-based imaging analysis pipeline involving baseline regression of motion parameters (i.e. tsoc+motreg) and another prominent yet more recent task-based denoising procedure, glmdenoise (). we utilized two separate tasks (i.e. the ‘selfother’ and ‘stories’ tasks) assessing neural systems supporting the social-cognitive domain or mentalizing and theory of mind […]


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GLMdenoise institution(s)
School of Psychology, University of Birmingham; Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK; Department of Psychology, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; Center for Magnetic Resonance Research (CMRR), Department of Radiology, University of Minnesota, Minneapolis, MN, USA
GLMdenoise funding source(s)
Supported by an European Research Council (ERC) Starting Grant ERC-2017-StG 759432, by an UK Medical Research Council Grant MC-A060-5PR60 and an ERC Starting Grant ERC-2010-StG 261352, and by the McDonnell Center for Systems Neuroscience and Arts & Sciences at Washington University.

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