Change Your Mind, Change the World

Center for Healthy Minds

University of Wisconsin–Madison
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​Tools for Scientists

Open-source ideas, research tools, tasks and data shared by our researchers and scholars

Data Analysis

Fmripower Tool

FMRIpower was introduced in a 2007 OHBM Poster and is based on the power analysis technique described by Jeanette Mumford and Thomas Nichols. This software is intended for use in study design, such as in the preparation of a grant application. It is not statistically appropriate to use a power analysis to assess the power of a study that has already taken place, but it can be used as a guide for planning future studies

Access the tool on Center Associate Scientist Jeanette Mumford's website.

Libraries for Reading BIOPAC Files

These utilities are for reading the files produced by BIOPAC’s AcqKnowledge software. Much of the information is based on Application Note 156 from BIOPAC; however, newer file formats were decoded by John Ollinger and Nate Vack.

This library is mostly concerned with getting the user the data, and less so with interpreting UI-related header values.

Learn more about this tool from Center "Hacker-in-Chief," Nate Vack.

Optimus

Optimus is a simple tool designed to convert experimental data from PST's E-Prime into a tab-delimited format for easy analysis.

Learn more about this tool, via Nate Vack.

Scatterize

Scatterize lets you upload a CSV file, plot the data, and in your browser in real-time, exclude outlier points and include nuisance variables. Every variation of your plot gives you a distinct URL, so you can prepare your chart and send it to a colleague.

Learn more and access the tool, also via Nate Vack.

scorify

Do you have questionnaire data with complicated scoring rules? Do you pull your hair out writing R code to score your data as you analyze it, only to find an mistake when you're half done with your paper? If so, scorify is for you. With scorify, you can quickly build a spreadsheet to clearly and reproducibly score all of your self-report data.

You can review the code here.

Datasets

Midlife in the United States (MIDUS) Study Data

Data and documentation for MIDUS 1MIDUS 2MIDUS 3, and all MIDUS projects are available at the Inter-university Consortium for Political and Social Research (ICPSR). To learn more about ICPSR visit their Homepage

Neonatal DTI Fiber Atlas

The neonatal DTI fiber atlas is for studies of brain development at birth and was created by the UNC Early Brain Development Studies (EBDS) group and NIRAL (Neuro Image Research and Analysis Laboratory).

The Neonate DTI atlas has a comprehensive set of template fibers for semi-automatic, tract-based analysis that represents a typically developing human brain during the first few weeks of life. It is believed to be the first population atlas with this magnitude of quality and sample size.

These resources enable widespread application of a set of template fibers for atlas-based, along-tract analysis that supports an adequate and reliable analysis of DTI in newborns in both practice and in clinical research settings to help address a critical gap in the current research community.

Access the data.

From the peer-reviewed paper: Amygdala and ventromedial prefrontal cortex are inversely coupled during regulation of negative affect and predict the diurnal pattern of cortisol secretion among older adults

Urry, H.L., van Reekum, C.M., Johnstone, T., Kalin, N.H., Thurow, M.E., Schaefer, H.S., Jackson, C.A., Frye, C.J., Greischar, L.L., Alexander, A.L., & Davidson, R.J. (2006). Amygdala and ventromedial prefrontal cortex are inversely coupled during regulation of negative affect and predict the diurnal pattern of cortisol secretion among older adults. Journal of Neuroscience, 26, 4415-4425. 

Access the data.

From the peer-reviewed paper: Gaze fixations predict brain activation during the voluntary regulation of picture-induced negative affect

van Reekum, C. M., Johnstone, T., Urry, H. L., Thurow, M. E., Schaefer, H. S., Alexander, A. L., & Davidson, R. J. (2007). Gaze fixations predict brain activation during the voluntary regulation of picture-induced negative affect. NeuroImage, 36, 1041-1055. 

Access the data.

From the peer-reviewed paper: Individual differences in some (but not all) medial prefrontal regions reflect cognitive demand while regulating unpleasant emotion

Urry, H. L., van Reekum, C. M., Johnstone, T., & Davidson, R. J. (2009). Individual differences in some (but not all) medial prefrontal regions reflect cognitive demand while regulating unpleasant emotion. NeuroImage, 47, 852-863.

Access the data.


Tips and Resources

MumfordBrainStats

Watch video tutorials from Associate Scientist Jeanette Mumford on common fMRI data and statistics conundrums. You can also join her Facebook group dedicated to brain statistics.

Video Games

Crystals of Kaydor

A team of researchers and game designers, led by Richard Davidson and Center Collaborator Constance Steinkuehler, developed the video game Crystals of Kaydor from the ground up aimed at teaching children pro-social behaviors, including recognizing others’ emotions.

Learn more and watch a demo.

Tenacity

Tenacity is a meditation app designed to promote mental well-being through breath counting. In the game, the focus is on learning practices of well-being and self-regulation. Users relax and focus their breathing as they explore Greek ruins, Egyptian dunes and staircases that ascend into the skies.

Study Games

Redistribution Game

Center scientists developed a redistribution game to study the impact of compassion training. The game requires hosting on a separate server and is not being actively updated.

Access the Redistribution Game.



Well-Being Interventions

Breath-Counting Task

Center researchers developed an online breath counting practice that can be used to train mindfulness. Our findings suggest that mindfulness, as measured through breath counting, is associated with more self-awareness, less mind wandering, better mood and more freedom from entrapping emotions.

Note: Turn on your audio to use this tool.

See the tool, courtesy of Daniel Levinson, Nate Vack and Sonam Kindy.

Compassion Meditation Training Audio Files

Compassion is the feeling of caring for and wanting to help others who are suffering. The following audio files and scripts were created as part of a study into the effectiveness of compassion meditation conducted by principal investigator Helen Weng with Drew Fox, Alex Shackman, Diane Stodola, Jessica Kirkland Caldwell, Matt Olson, Greg Rogers and Richard Davidson.

Cognitive Reappraisal Training

Cognitive reappraisal is learning to re-interpret the meaning of situations to decrease negative emotions and stress. This 30-minute reappraisal training was used as a control intervention for compassion meditation and teaches three new ways of looking at situations: understanding from another person’s perspective, adopting a new perspective yourself and looking at the situation as if a year had gone by. This training is based on cognitive-behavioral therapy, which has been shown to be an effective treatment for conditions such as depression and anxiety.