Blog Archives

fslr: An R Package Interfacing with FSL for Neuroimaging Analysis

June 16, 2014
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fslr: An R Package Interfacing with FSL for Neuroimaging Analysis

I use a set of neuroimaging tools, but my language of choice is R. FSL, which is from the University of Oxford's Functional MRI of the Brain (FMRIB), and stands for FMRIB Software Library, is one tool I commonly use. I wrote some wrapper functions into an R package called fslr and wanted to discuss

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Making Back-to-Back Histograms

June 10, 2014
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Making Back-to-Back Histograms

A colleage of mine asked me how to do back to back histograms (instead of on top of each other). I feel as though there should be a function like voilin plot from the vioplot package. Voilin plots are good for displaying data, but the violin must have the left and right (or top and

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SMART Hackathon: Day 2: Writing Packages in RStudio

May 6, 2014
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SMART Hackathon: Day 2: Writing Packages in RStudio

So day 2 of the #JHUSMARTHack was last week, but I figured this would be a good time to discuss what was accomplished. I created some packages that are somewhat specialized and aren't fully finished yet, so I'll hold off. What I really want to discuss though is why I like using RStudio for making

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SMART Hackathon: Day 1

May 1, 2014
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SMART Hackathon: Day 1

So day 1 of the #JHUSMARTHack 2014 is over and day 2 is underway. It's been awesome. One student estimated he did “one week's worth of work”. Some interesting (I think) things I thought about: Flooding rain is good weather for coding. (As long as no sinkholes arise) The Admiral Fell Inn is a pretty

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SMART Hackathon 2014

April 30, 2014
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SMART Hackathon 2014

Today is our SMART group's 2014 Hackathon! We will be at an undisclosed location, just plugging away at code/packages/apps. The mission statement: There's no structure except that you have to work on a software project and you have to present what you accomplished or didn't at a subsequent SMART meeting. We will be tweeting at

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brainR: Put your brain on the Cloud!

April 29, 2014
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brainR: Put your brain on the Cloud!

In my work, we have come across problems where we wanted to visualize data in 4 dimensions (4D). The data came as brains, which are represented as 3D volumes and we wanted to visualize them at different time points (hence 4D). We were using images that are acquired one image per visit (CT structural scans,

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ENAR 2014 Searcher #ENAR2014

March 12, 2014
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ENAR 2014 Searcher #ENAR2014

To those going to ENAR this year: Are you trying to find who’s presenting at ENAR from your department but all that pdf searching got you down?  Are you trying to make an itinerary but dislike copying and pasting from a pdf?  Well I have a Shiny App for you! At https://muschellij2.shinyapps.io/ENAR_2014, you can see all

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