Center for Healthy Minds | 625 W. Washington Ave., Madison, WI 53703-2637
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.
Bioread
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.
Hedonometer
Much of traditional psychology research involves bring participants to the lab and having them fill out various questionnaires. Then, researchers correlate their questionnaire answers with other data acquired in the lab.
Many variants on experience sampling exist; however, extant ones tend to rely either on specialized hardware and/or software, or online connectivity. Hedonometer differs in that participants are prompted for and send data purely by text message. Hence, people need only have a cell phone to participate.
Masterfile
Tools to organize, access, and catalog the variables of interest in a scientific study.
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 a 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.
Datasets
Midlife in the United States (MIDUS) Study Data
Data and documentation for 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.
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.
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.
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.
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.
Emotional Styles Questionnaire Research Tool
The research tool yields scores for six emotional dimensions -- resilience, outlook, social intuition, self-awareness, sensitivity to context, and attention -- which can be traced to specific brain circuits. It also results in an overall score of healthy emotionality, which is the average of the six dimensions. The 24 question questionnaire as a whole acts as a summary assessment of a person’s emotional well-being.
Learn more and download the tool.
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
Heath Enhancement Program
The Health Enhancement Program was created as an active control for Mindfulness Based Stress Reduction (MBSR). The program is well-matched with MBSR, but does not have a mindfulness component.
Healthy Minds Program
The Center for Healthy Minds has created a new scientific framework for understanding how human flourishing can be nurtured consisting of four pillars of well-being: awareness, connection, insight and purpose. Research shows that each of these four pillars are related to specific networks in the brain and can be strengthened through meditation and other forms of mental training. Learn more about the framework.
For those interested in using the Healthy Minds Program in a study or intervention, please fill out this form to be put in touch with Healthy Minds Innovations, who created the Healthy Minds Program.
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.