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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.

Posts

Neurostuff Development Environment

2 minute read

Published: September 10, 2020

This post is a chronicle of how I’m setting up a development environment for neurostuff using VSCode (version 1.48.2 as of this writing).

Development Environment with VS Code

7 minute read

Published: June 26, 2019

Often times you have to choose between installing the complex web of dependencies to debug fmriprep from a graphical text editor and using a container where you can only debug from a terminal. VS Code has several extensions that make it easier to develop fmriprep and have the best of both worlds. The VS Code Docker and Remote Development extensions will give you a great experience running tests and debugging fmriprep on your laptop or work machine.

Rules for problem solving and understanding code

less than 1 minute read

Published: April 06, 2019

Create a minimal dataset to test the code

Python User Learning R

1 minute read

Published: February 05, 2019

Just as I’m getting a feel for python, why not tack on another language. R is very popular for statistical computing, and the number of packages R has for this functionality confirms that intuition.

Automating Data Quality Assurance

20 minute read

Published: November 20, 2018

This is an ongoing process where we are attempting to collect data and visualize it quickly so we can see if anything looks off.

My Workflow

1 minute read

Published: October 14, 2018

We work with data on a lab server, basically network attached storage… There is no ftp access or any other web service integrations, so we do not treat it as our own private git server. However, I am “softly” mimicking that functionality in my current workflow. Once I’ve generated data I want to analyze/explore on the server (via some heavy data chugging analysis through the cluster), I can make the output directory a git repository and clone it locally. Since multiple people can access the server at the same time, this is useful as to not step on each other’s toes as we access/modify data. When I’m done fooling around locally, I can try to push, but since the repository I cloned from isn’t bare, I can’t. To get around that I had to use this command (that I stole from stack overflow):

portfolio

NeuroSynth 2.0

Modernizing automated meta-analysis with scalable NLP/LLM-assisted literature pipelines.

Neurosynth Compose

Web platform for transparent, reproducible neuroimaging meta-analysis.

NiMARE

Python ecosystem for coordinate- and image-based neuroimaging meta-analysis.

Open Science, Standards, and Mentoring

Teaching, community-building, and standards-based tooling (e.g., BIDS) that make research more reusable.

publications

Carotid Beta-stiffness index is associated with slower processing speed but not working memory or white matter integrity in healthy middle-aged/older adults

Published in Journal of Applied Physiology, 2017

Association between carotid stiffness and processing speed in healthy aging.

Recommended citation: DuBose, L. E., Voss, M. W., Weng, T. B., Kent, J. D., Dubishar, K. M., Lane-Cordova, A., Sigurdsson, G., Schmid, P., Pierce, P. B., Barlow, P. T., & Pierce, G. L. (2017). “Carotid Beta-stiffness index is associated with slower processing speed but not working memory or white matter integrity in healthy middle-aged/older adults.” Journal of Applied Physiology, 122(4), 868–876.
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fMRIPrep: a robust preprocessing pipeline for functional MRI

Published in Nature Methods, 2019

Automated, analysis-agnostic preprocessing for fMRI with transparent visual reports.

Recommended citation: Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A. I., Erramuzpe, A., Kent, J. D., et al. (2019). “fMRIPrep: a robust preprocessing pipeline for functional MRI.” Nature Methods, 16(1), 111–116.
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Home-Based, Adaptive Cognitive Training for Cognitively Normal Older adults: Initial Efficacy Trial

Published in The Journals of Gerontology: Series B, 2019

Randomized trial evaluating a home-based adaptive cognitive training intervention.

Recommended citation: Lee, H. K., Kent, J., Wendel, C., Wolinsky, F., Foster, E., Merzenich, M., & Voss, M. (2019). “Home-Based, Adaptive Cognitive Training for Cognitively Normal Older adults: Initial Efficacy Trial.” The Journals of Gerontology: Series B.
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NiBetaSeries: task related correlations in fMRI

Published in Journal of Open Source Software, 2019

Open-source tooling for beta-series correlation analyses in fMRI.

Recommended citation: Kent, J., & Herholz, P. (2019). “NiBetaSeries: task related correlations in fMRI.” Journal of Open Source Software, 4(41), 1295.
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Analysis of task-based functional MRI data preprocessed with fMRIPrep

Published in bioRxiv, 2020

Protocol for integrating fMRIPrep into task-based fMRI workflows.

Recommended citation: Esteban, O., Ciric, R., Finc, K., Blair, R., Markiewicz, C. J., Moodie, C. A., Kent, J. D., et al. (2020). “Analysis of task-based functional MRI data preprocessed with fMRIPrep.” bioRxiv.
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Neurosynth Compose: A web-based platform for flexible and reproducible neuroimaging meta-analysis

Published in Imaging Neuroscience, 2026

Neurosynth Compose is a web platform for transparent, reproducible neuroimaging meta-analysis.

Recommended citation: Kent, J. D., Lee, N., Laird, A. R., Salo, T., Peraza, J., Bottenhorn, K. L., Oudyk, K., Nichols, T. E., Poline, J.-B., & de la Vega, A. (2026). “Neurosynth Compose: A web-based platform for flexible and reproducible neuroimaging meta-analysis.” Imaging Neuroscience, 4, IMAG.a.1114.
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