zeigar / spin-test

This toolbox includes MATLAB scripts to perform a "spin test" of anatomical correspondence between cortical surface maps, as presented in "On testing for spatial correspondence between maps of human brain structure and function," Alexander-Bloch et al., NeuroImage, 2018.

Spin Test

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.

Please contact us at [email protected]

Contents:

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

Requirements:

1. FreeSurfer Matlab toolbox for FreeSurfer IO and it is included in FreeSurfer installation
2. Toolbox SurfStat (included in scripts directory) for CIVET IO,
   http://www.bic.mni.mcgill.ca/ServicesSoftware/StatisticalAnalysesUsingSurfstatMatlab
3. Nearestneighbour.m included in scripts directory, https://www.mathworks.com/matlabcentral/fileexchange/12574-nearestneighbour-m

Tutorials:

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1. Run DemonSpinFS.m Demonstrate how spin rotation works with a faked dataset in FreeSurfer fsaverage5.
2. Run SpinPermuFS.m Generate the null distribution of the map in FreeSurfer by randomly spinning user-defined # times. See example included in this code.
3. Run SpinPermuCIVET.m Generate the null distribution of the map in CIVET by randomly spinning user-defined # times. See example included in this code.
4. Run pvalsNull.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, Simon Vandekar & Siyuan Liu.

Related Projects:

1. An implementation specifically for parcellated brain maps, by František Váša:

• Váša F., Seidlitz J., Romero-Garcia R., Whitaker K. J., Rosenthal G., Vértes P. E., Shinn M., Alexander-Bloch A., Fonagy P., Dolan R. J., Goodyer I. M., the NSPN consortium, Sporns O., Bullmore E. T. (2017). Adolescent tuning of association cortex in human structural brain networks. Cerebral Cortex, 28(1):281–294.
• https://github.com/frantisekvasa/rotate_parcellation

Notes:

Initial commit: 2018-04-22

UPDATE 2018-07-18

• bug fix to implement improved method of random rotations, as original method had a preference for certain rotations
• see technical note for details.

UPDATE 2019-06-18

• now using Richard Brown's nearestneighbour function, which saves substantial time compared to our own implementation especially with larger surface files.

UPDATE 2020-08-24 thanks to Sarah Weinstein (https://github.com/smweinst)

• Changes default to set medial wall to NaN, as opposed to leaving this up to user.
• In SpinPermuFS.m, added code to import the annotation files for fsaverage5 that are part of the medial wall, and replace those vertices with NaN
• In pvalsNull.m, the user now has to input a vector of 0s/1s to indicate which vertices are part of the medial wall
• Also fixed bug in pvalsNull.m to add abs() around the null and real rho values used for computing the p-values
• Note that these changes are for Freesurfer version only, but we recommend this framework for CIVET surfaces as well