#knitr — Public Fediverse posts

I posted a new introduction to surface #gifti and volume #NIfTI #fMRI data at https://mvpa.blogspot.com/2025/01/intro-to-working-with-volume-and.html.

The material is mostly general, with all examples using #baseR #rstats code; it's accompanied by a major update to my gifti #knitr tutorial.

I hope these will be useful to folks getting started with #neuroimaging datasets, as well as anyone looking for example scripts for reading, plotting, and manipulating (human fMRI) brain data files.

I posted a new introduction to surface #gifti and volume #NIfTI #fMRI data at https://mvpa.blogspot.com/2025/01/intro-to-working-with-volume-and.html.

The material is mostly general, with all examples using #baseR #rstats code; it's accompanied by a major update to my gifti #knitr tutorial.

I hope these will be useful to folks getting started with #neuroimaging datasets, as well as anyone looking for example scripts for reading, plotting, and manipulating (human fMRI) brain data files.

Major thanks to @tannguyen for spotting and reporting a bug in my niftiPlottingFunctions.R plot.volume() function!

The code at https://osf.io/k8u2c is updated; see https://mvpa.blogspot.com/2023/03/bugfix-for-niftiplottingfunctionsr.html for info and examples.

(This #baseR #rstats function is for plotting #fMRI #nifti images in #knitr documents.)

... it is painful to find out there was a bug, but so much better to fix it than to continue its propagation! I am grateful to @tannguyen and hope anyone else seeing something odd lets me know.

A methods paper of mine is now at https://doi.org/10.3389/fnimg.2023.1070274 . This little #NewNeuroPaper demonstrates human task #fMRI quality control, as part of the FMRI Open QC Project (which I hope to discuss at #OHBM and elsewhere as it wraps up).

Its supplemental (https://doi.org/10.17605/OSF.IO/HT543) may be of interest to #rstats folks, particularly if looking for examples of #baseR #knitr #graphics and/or scripts aiming to minimize dependencies and maximize long-term usability.

A methods paper of mine is now at https://doi.org/10.3389/fnimg.2023.1070274 . This little #NewNeuroPaper demonstrates human task #fMRI quality control, as part of the FMRI Open QC Project (which I hope to discuss at #OHBM and elsewhere as it wraps up).

Its supplemental (https://doi.org/10.17605/OSF.IO/HT543) may be of interest to #rstats folks, particularly if looking for examples of #baseR #knitr #graphics and/or scripts aiming to minimize dependencies and maximize long-term usability.

@ERDonnachie @tgtads @datamaps

I can't resist a #tidyverse vs. #baseR #rstats thread. 😅

It is totally possible to work without tidyverse, and base R graphics can be incredibly flexible. If you'd like some examples, just this morning I uploaded yet another set of all-base #knitr supplemental files (https://osf.io/ht543), with very pretty (and highly useful) graphics, if I say so myself. (Tidyverse can be ok, but it's not at all required.)

@ERDonnachie @tgtads @datamaps

I can't resist a #tidyverse vs. #baseR #rstats thread. 😅

It is totally possible to work without tidyverse, and base R graphics can be incredibly flexible. If you'd like some examples, just this morning I uploaded yet another set of all-base #knitr supplemental files (https://osf.io/ht543), with very pretty (and highly useful) graphics, if I say so myself. (Tidyverse can be ok, but it's not at all required.)

#papaja, #rstats and #knitr people: Can you change line spacing and font when knitting to PDF? Been collaborating on a paper, and we've knitted to PDF by default. Ended up just below 40 pages - perfect! But a submission deadline is nearing, and we needed a word version. Turns out it is at 45 pages! Done side-by side comp. Seems the PDF is not Times New Roman. Also, line spacing is different. We get around 27 lines on a PDF page, but 24 in the Word version. Ideas? @FrederikAust

#papaja, #rstats and #knitr people: Can you change line spacing and font when knitting to PDF? Been collaborating on a paper, and we've knitted to PDF by default. Ended up just below 40 pages - perfect! But a submission deadline is nearing, and we needed a word version. Turns out it is at 45 pages! Done side-by side comp. Seems the PDF is not Times New Roman. Also, line spacing is different. We get around 27 lines on a PDF page, but 24 in the Word version. Ideas? @FrederikAust

#introduction

I'm a staff scientist at Washington U in St Louis (#WashU #wustl #Missouri, USA), mostly working with human task fMRI datasets. I'm a big fan of #baseR and #knitr #rstats, #QC, and very extensive #supplementary materials. I insist on looking at data early and often; some #tutorials and examples on my blog. (#GotBrains?)

I'm a #FirstGen college grad, #IowaStateU; BS in #forestry. I also occasionally share cats, #knitting, and #crochet. Promoting abortion rights, not book bans.

#introduction

I'm a staff scientist at Washington U in St Louis (#WashU #wustl #Missouri, USA), mostly working with human task fMRI datasets. I'm a big fan of #baseR and #knitr #rstats, #QC, and very extensive #supplementary materials. I insist on looking at data early and often; some #tutorials and examples on my blog. (#GotBrains?)

I'm a #FirstGen college grad, #IowaStateU; BS in #forestry. I also occasionally share cats, #knitting, and #crochet. Promoting abortion rights, not book bans.