R for Neuroscientists

Courses & Tutorials Only

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fNIRS & NIRS

fMRi, MRI, & qMRI

Working with fMRI data using R

Added Sunday Dec 13th, 2020

What is this?
Description from site: Reading and visualising fMRI data with R/neuroconductor.

1. Link to site: https://jokedurnez.github.io/validating-fmri/01-introduction/index.html

R for statistical analysis of fMRI data

By Tara Madhyastha

Added Sunday Dec 13th, 2020

What is this?

Tutorial given at Neurohackademy 2018 by Tara Madhyastha

1. Link to site in NeuroHackademy: https://neurohackademy.org/course/r-for-statistical-analysis-of-fmri-data/
2. Link to youtube video: https://youtu.be/sdbkWvFhTZ0

EEG

All Neuro

neuropointillist

Added Sunday Dec 13th, 2020
What is this?

Description from site: Flexible modeling of neuroimaging data in R, point by point

1. Link to site: http://ibic.github.io/neuropointillist/
2. Content:

• Simple fMRI example
• Advanced fMRI example
• Permutation testing fMRI example
• Flournoy example (longitudinal)
• Correcting for multiple comparisons

Plotting brain atlases in ggplot

Added Sunday Dec 13th, 2020
What is this?

Description from site: Plotting regions from different brain atlases ggplot2 is a handy way of displaying results or grouping of aparc data.

The function ggseg(), is based in the ggplot2 format, it is recommended to get familiarized with plotting data with ggplot2.

Out-of-the-box, ggseg() works without supplying any extra information. It will create a base plot of the aparc brain segmentations.

1. Link to site: https://lcbc-uio.github.io/ggseg/articles/ggseg.html
2. Link to ggseg vignette: https://github.com/LCBC-UiO/ggseg/blob/master/vignettes/ggseg.Rmd
3. Link to ggseg repo: https://github.com/LCBC-UiO/ggseg

Neuroconductor

Added Sunday Dec 13th, 2020
What is this?

Description from site: Neuroconductor is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to:

provide a centralized repository of R software dedicated to image analysis; disseminate quickly software updates; educate a large, diverse community of scientists using detailed tutorials and short courses; ensure quality via automatic and manual quality controls; and promote reproducibility of image data analysis. Based on the programming language R, Neuroconductor started with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing.

1. Link to site here: https://neuroconductor.org/

Neuroimaging Analysis within R

Added Sunday Dec 13th, 2020
What is this?

Series of slides with code for course on Neuroimaging Analysis: All the PDF slides are located in a zip file here.

• Introduction and R Slides, PDF Slides, R Code, Source
• General R (not covered at ENAR) Slides, PDF Slides, R Code, Source
• Imaging Packages in R Slides PDF Slides, R Code, Source
• Visualization of Images Slides PDF Slides, R Code, Source
• Inhomogeneity Correction Slides, PDF Slides, R Code Source
• Brain Extraction/Segmentation Slides, PDF Slides, R Code, Source
• Image Registration Slides PDF Slides, R Code, Source
• Tissue-Class Segmentation Slides PDF Slides, R Code, Source
• Intensity Normalization Slides, PDF Slides, R Code, Source
• Segmentation of MS Lesions Slides, PDF Slides, R Code, Source
• Image Harmonization Slides PDF Slides, R Code, Source
• Starting with Raw (DICOM) Data (not covered) Slides, PDF Slides, R Code, Source

1. Link to site here: https://johnmuschelli.com/imaging_in_r/