Useful links

Beautiful graphs using R

https://rstudio-pubs-static.s3.amazonaws.com/228019_f0c39e05758a4a51b435b19dbd321c23.html#31_box_plots

Guidelines for Presenting Neuroimaging Analyses

https://warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/research/bestpractice/http://www.humanbrainmapping.org/files/2016/COBIDASreport.pdf

The scientist’s english

https://www.shearsoneditorial.com/the-scientists-english/

Shell scripting
https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/scripting/all.htm

Bash beginners guide

http://www.tldp.org/LDP/Bash-Beginners-Guide/html/sect_07_01.html

Life in a shell – Tom Nichols’ Linux tips for scientific computing

https://warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/Life_in_a_Shell.pdf

UsefulFSLmaths commands
http://www.smart-stats.org/wiki/some-useful-fsl-commands

https://mandymejia.wordpress.com/fsl-maths-commands/
FSLutils
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/tutorial_packages/OSX/fsl_501/doc/wiki/Fslutils.html
FSL cluster
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster

TIPS ON STATS

MUMFORD BRAIN STATS YOUTUBE CHANNEL
https://www.youtube.com/channel/UCZ7gF0zm35FwrFpDND6DWeA

Best practices in data analysis and sharing in neuroimaging using MRI

Main paper (COBIDAS Nichols et al., 2016):
https://www.nature.com/articles/nn.4500Other documents:
https://www.biorxiv.org/content/10.1101/054262v1http://www.humanbrainmapping.org/files/2016/COBIDAS-Final%20For%20Vote.pdf

Guidelines on reporting an fMRI study (Poldrack et al., 2008)
https://www.ncbi.nlm.nih.gov/pubmed/18191585

Inference
https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/feat2_part2.pdf

https://warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/publications/books/poldrack_mumford_nichols-do-not-distribute/fmri_book_-c07_p110-129.pdf

no correction < FDR voxel-wise < FDR cluster-wise < FWE cluster-wise < FWE voxel-wise

Bibliometrics of cluster inference
https://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/

P threshold FAQ NEUROIMAGING

http://mindhive.mit.edu/book/export/html/90
https://www.ohbmbrainmappingblog.com/blog/keep-calm-and-scan-on

Thresholding with Random Field Theory

http://lsr-wiki-01.mrc-cbu.cam.ac.uk/imaging/PrinciplesRandomFields

Thread on FSL’s mailing list discussing Eklund et al. 2016 cluter failure paper (dangers of clusterwise inference done wrong)

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1607&L=spm&D=0&P=159892

RANDOMISE FSL (non parametric statistical analysis)
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise/UserGuidehttps://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomisehttps://www.youtube.com/watch?v=Ukl1VWobviw

Add additional contrasts in randomise without having to rerun everything

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;91ea4524.1402
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1402&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=282189