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This toolbox includes scripts to perform a "spin test" of anatomical correspondence between 
cortical surface maps in either FreeSurfer or CIVET. 
These methods are described in "On testing for spatial correspondence between maps of 
human brain structure and function," Alexander-Bloch et al., NeuroImage, 2018.

Contents:
data/ directory contains files needed to run scripts
script/ directory includes all m files 

Requirements:
1) AxelRot.m (included in scripts directory) from file exchange, 
https://www.mathworks.com/matlabcentral/fileexchange/30864-3d-rotation-about-shifted-axis
2) FreeSurfer Matlab toolbox for FreeSurfer IO and it is included in FreeSurfer installation 
3) Toolbox SurfStat (included in scripts directory) for CIVET IO,  
http://www.bic.mni.mcgill.ca/ServicesSoftware/StatisticalAnalysesUsingSurfstatMatlab

Tutorials:
---------
1 Run DemonSpinFS.m
Demonstrate how spin rotation works with a faked dataset in FreeSurfer fsaverage5.
2a Run SpinPermuFS.m
Generate the null distribution of the map in FreeSurfer by randomly spinning user-defined # times
See example included in this code.
2b Run SpinPermuCIVET.m
Generate the null distribution of the map in CIVET by randomly spinning user-defined # times
See example included in this code.
3 Run pvalvsNull.m
Calculate the p-value of correlation between two surface maps based on
the null distribution of spins of map 1, output from 2a or 2b.
See example included in this code.

This toolbox was developed and tested under Matlab R2015a by Aaron Alexander-Bloch & Siyuan Liu.

2018-04-22