Erik Barry Erhardt, PhD

We got one! Research Allocation Committee (RAC) Grants are for supporting new research or creative works. The RAC is particularly supportive of projects that may lead to outside funding and/or larger related projects.

PIs: Erik Erhardt and David Hanson
Title: “Frequentist (bootstrap) and Bayesian modeling of (photo)respiration in plants”
Amount: $3982.63, RAC 12-04
Use: To hire statistics graduate student, Mohammad Hattab, to implement and develop modeling that I did last summer in Switzerland.

Purpose:
We are requesting $3982.63 to develop statistical models to estimate (photo)respiration in plants, accounting for sources of uncertainty and prior information. Because current models provide estimates without meaningful assessments of uncertainty, our model will have broad application in understanding photosynthetic pathways and carbon usage in plants, clarifying the precision of our knowledge, conditional on what is already believed. This modeling is an important step towards developing more comprehensive models of photosynthetic parameters. Support from the Resource Allocation Committee will allow us to: (1) develop frequentist (bootstrap) and Bayesian models to analyze existing experimental data, providing inferences on the set of parameters related in the model; (2) design experiments and acquire additional data to distinguish and estimate respiration and photorespiration under a set of scientifically relevant conditions; (3) conduct validations using pre-existing data and estimates; (4) publish our model with results; and (5) develop grant proposals to apply this model more broadly.

Research, stable isotopes, Statistics

Modular organization of functional network connectivity in healthy controls and patients with schizophrenia during the resting state
Qingbao Yu, Sergey M Plis, Erik B Erhardt, Elena A Allen, Jing Sui, Kent A Kiehl, Godfrey Pearlson, Vince D Calhoun
2011 Frontiers in Systems Neuroscience

Abstract
Neuroimaging studies have shown that functional brain networks composed from select regions of interest (ROIs) have a modular community structure. However, the organization of functional network connectivity (FNC), comprising a purely data-driven network built from spatially independent brain components, is not yet clear. The aim of this study is to explore the modular organization of FNC in both healthy controls (HCs) and patients with schizophrenia (SZs). Resting state functional magnetic resonance imaging (R-fMRI) data of HCs and SZs were decomposed into independent components (ICs) by group independent component analysis (ICA). Then weighted brain networks (in which nodes are brain components) were built based on correlations between ICA time courses. Clustering coefficients and connectivity strength of the networks were computed. A dynamic branch cutting algorithm was used to identify modules of the FNC in HCs and SZs. Results show stronger connectivity strength and higher clustering coefficient in HCs with more and smaller modules in SZs. In addition, HCs and SZs had some different hubs. Our findings demonstrate altered modular architecture of the FNC in schizophrenia and provide insights into abnormal topological organization of intrinsic brain networks in this mental illness.

MIND, Research

My AmWeek 2011 calling and teaching highlights: Karina and I leading couples dancing with Crowfoot, calling a techno contra, calling for camper open mic, free-form calling in evenings with Will Mentor.

(I’ll be teaching couples dance again at AmWeek 2012!)

Eric Black and Diane Zingale with many other organizers created an amazing AmWeek 2011. Visit the website and fb page and join us for AmWeek 2012! See Photos.

Mary Wesley and I attended morning calling session for squares with Will Mentor and contra with Erik Weburg. Will gave me the opportunity to mimic his freeform squares from the first night. Erik suggested that I be a little more assertive in my calling (rather than saying things in a question-sounding way).

In the afternoons, Karina Wilson and I lead couples dance workshops with the moving music of Crowfoot (Jaige, Adam, and Nickolas). The first day was waltz and moves from uncrossed-hands position, including the cuddle. The second day we did Scandinavian dance, including the Snoa and the Hambo. The last day we continued waltz with moves from crossed-hands position, including cape and skaters. In an additional “waltz-swap” session, dancers “traded licks”, which is such a great idea at dance camps with so many talented dancers.

Dance teaching handouts: waltz hambo

I got picked to call the techno contra, too. What a great surprise! I called a medley of 3 dances to music that Katie Hepp brought to camp, and Will djed (clicked “play”) from his Mac. Because the music is loud and it’s a medley, I found it helped to call most of the calls all the way through each turn of the dance, only dropping calls for “hook” moves, and having additional prompts like, “something new” or “listen up”, before transitioning to the next dance in the medley. It was more challenging to call because I was behind the speakers and couldn’t hear the music as well as I can with a live band; a monitor with the same mix as the floor would be helpful to hear both the music and my voice.

And some exciting news for me from the BACDS newsletter Winter 2012 about “American Dance & Music Week 2012″:

“Couple dancing including waltzes and other styles will be taught by returning teacher Erik Erhardt. Erik was very well received last July, and we’ve asked him to come back and do it again.”

To be invited back is the biggest complement!

The previous year, 2010, Joyce Miller and Joyce Cooper made sure we were well taken care of! Joyce Cooper, especially, went way out of her way to have a van at the airport parking lot for me and my five wonderful Santa Fe girls. Then, on the way home, Eric Black saved us by giving us (me, Karina, Laurel, Lauren, Mia, Zoe, Chelsea, Tank, Andrew) an emergency place to slumber and threw in an extra “Get out of Hell, free” card, which I hope I don’t have to use with him again… Eric and Diane’s thoughtful caring really makes life wonderful for those around them.

dance, Fun

Our paper detailing our simulation toolbox (SimTB) has been published in NeuroImage.

SimTB, a simulation toolbox for fMRI data under a model of spatiotemporal separability
Erik B. Erhardt, Elena A. Allen, Yonghua Wei, Tom Eichele, Vince D. Calhoun
NeuroImage 59 (2012), pp. 4160-4167
Received at Elsevier: 29 Nov 2011, Available online 8 Dec 2011, published online 5 Jan 2012
ISSN 1053-8119, 10.1016/j.neuroimage.2011.11.088
(http://dx.doi.org/10.1016/j.neuroimage.2011.11.088)
http://www.sciencedirect.com/science/article/pii/S105381191101370X
Keywords: simulation; fMRI; group analysis

SimTB flowchart for simulation of fMRI data

Abstract
We introduce SimTB, a MATLAB toolbox designed to simulate functional magnetic resonance imaging (fMRI) datasets under a model of spatiotemporal separability. The toolbox meets the increasing need of the fMRI community to more comprehensively understand the effects of complex processing strategies by providing a ground truth that estimation methods may be compared against. SimTB captures the fundamental structure of real data, but data generation is fully parameterized and fully controlled by the user, allowing for accurate and precise comparisons. The toolbox offers a wealth of options regarding the number and configuration of spatial sources, implementation of experimental paradigms, inclusion of tissue-specific properties, addition of noise and head movement, and much more. A straightforward data generation method and short computation time (3–10 seconds for each dataset) allow a practitioner to simulate and analyze many datasets to potentially understand a problem from many angles. Beginning MATLAB users can use the SimTB graphical user interface (GUI) to design and execute simulations while experienced users can write batch scripts to automate and customize this process. The toolbox is freely available at http://mialab.mrn.org/software together with sample scripts and tutorials.

Keyword: simulation; fMRI; group analysis

MIND, Research