pestica:MainPage

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The tools in this distribution allow you to make signals corresponding to physiologic signals, and then correct for them. These are specific to echo-planar (traditional, not spiral at this time) MR imaging timeseries data, such as functional MRI or connectivity MRI, although this tool has also been used in arterial spin-labelled (ASL) timeseries data. PESTICA is our temporal ICA-based tool to detect physiologic signals and IRF-RETROICOR is our tool to correct a dataset for the noise sources (matlab version of Gary Glover's RETROICOR is also included as an optional script).

The PESTICA algorithm is described in Beall, Erik B, et al. Isolating physiologic noise sources with independently determined spatial measures. ''Neuroimage''. 2007 Oct 1; '''37''' (4):1286-300. The IRF-RETROICOR algorithm is described in Beall, Erik B. Adaptive cyclic physiologic noise modeling and correction in functional MRI. ''J Neurosci Methods''. 2010 Mar 30; '''187''' (2):216-28.

The newest version (PESTICA-afni-v1.2) supports the AFNI .BRIK format and the NIFTI .nii or .nii.gz formats.  This tool requires the phase-encoding direction be in the Anterior-Posterior direction and have reasonable temporal length of acquisition (at least 3 minutes).

PESTICA and IRF-RETROICOR have been used or are currently in use by several groups, including the Medical College of Wisconsin, NIH/NIDA Neuroimaging Research Branch, Central Institute of Mental Health Mannheim, Baylor College of Medicine Texas Medical Center, University Hospital Basel, Yale University and Medical University of Vienna Center for Biomedical Engineering and Physics.

PESTICA has been used for data analyses in the following articles: Wu, Changwei W, et al. Frequency specificity of functional connectivity in brain networks. ''Neuroimage''. 2008 Sep 1; '''42''' (3):1047-55., Lowe, Mark J, et al. Resting state sensorimotor functional connectivity in multiple sclerosis inversely correlates with transcallosal motor pathway transverse diffusivity. ''Hum Brain Mapp''. 2008 Jul; '''29''' (7):818-27., Beall, Erik B. Adaptive cyclic physiologic noise modeling and correction in functional MRI. ''J Neurosci Methods''. 2010 Mar 30; '''187''' (2):216-28., and Wu, Changwei W, et al. Mapping functional connectivity based on synchronized CMRO2 fluctuations during the resting state. ''Neuroimage''. 2009 Apr 15; '''45''' (3):694-701.

KNOWN ISSUES, see [1].