MRIdataviz

Supplementary to Pernet, C. R., & Madan, C. R. (in press). Data visualization for inference in tomographic brain imaging. European Journal of Neuroscience. doi: 10.1111/ejn.14430

Visualization

2D

ICBM 152 Nonlinear atlases version 2009

http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

xjView

http://www.alivelearn.net/xjview/

bspmview

http://www.bobspunt.com/bspmview/

nanslice

https://github.com/spinicist/nanslice

3D

mni2fs

https://github.com/dprice80/mni2fs

pySurfer

https://Pysurfer.github.io

Pycortex

https://github.com/gallantlab/pycortex

BrainBrowser

https://brainbrowser.cbrain.mcgill.ca

BrainNetBrowser

https://www.nitrc.org/projects/bnv/

ITK-SNAP

http://www.itksnap.org/

MRIcro, MRIcron, MRIcroGL, MRIcroS, Surf Ice

http://www.mccauslandcenter.sc.edu/crnl/tools

Interpretation

Shed

http://upenncmroi.wpengine.com/shed/

Color Palettes

Recommended Reading

https://mycarta.wordpress.com/2012/05/29/the-rainbow-is-dead-long-live-the-rainbow-series-outline/

cmocean

https://github.com/matplotlib/cmocean

http://www.mathworks.com/matlabcentral/fileexchange/57773-cmocean-perceptually-uniform-colormaps

http://matplotlib.org/cmocean/

Brewer

http://colorbrewer2.org

https://github.com/DrosteEffect/BrewerMap

https://www.mathworks.com/matlabcentral/fileexchange/45208-colorbrewer--attractive-and-distinctive-colormaps

http://www.mathworks.com/matlabcentral/fileexchange/30564-othercolor

mpl colormaps (viridis)

http://bids.github.io/colormap/

https://www.mathworks.com/matlabcentral/fileexchange/51986-perceptually-uniform-colormaps

https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html

https://www.youtube.com/watch?v=xAoljeRJ3lU

CET (Centre for Exporation Targeting)

http://peterkovesi.com/projects/colourmaps/

http://peterkovesi.com/MatlabFns/

https://github.com/bokeh/colorcet

https://arxiv.org/abs/1509.03700

pmkmp

https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps

https://github.com/mycarta/PMKMP

https://mycarta.wordpress.com/2013/03/06/perceptual-rainbow-palette-the-goodies/

https://mycarta.wordpress.com/2012/05/29/the-rainbow-is-dead-long-live-the-rainbow-series-outline/

bipolar

http://www.mathworks.com/matlabcentral/fileexchange/26026-bipolar-colormap

cubehelix

https://www.mrao.cam.ac.uk/~dag/CUBEHELIX/

http://www.mathworks.com/matlabcentral/fileexchange/43700-cubehelix-colormaps--beautiful--distinct--versatile-

Light & Bartlein

http://www.mathworks.com/matlabcentral/fileexchange/17555-light-bartlein-color-maps

Haxby

https://www.mathworks.com/matlabcentral/fileexchange/25690-haxby-color-map