Updated how drift is calculated and how masking is done (Ready for review)#244

Merged

mihaic merged 53 commits into

brainiak:masterfrom

CameronTEllis:fmrisim_mean_mask

Nov 10, 2017

Commits on Jul 21, 2017

Updated how drift is calculated and how masking is done
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PEP error
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Commits on Jul 22, 2017

Changed how cycles are calculated for drift
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PEP error and updated doc
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PEP error
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Commits on Jul 23, 2017

Updated doc string of most functions to be more clear. Combined _calc_sfnr and _calc_temporal_noise and then edited accordingly
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PEP errors
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PEP error
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PEP error
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PEP error
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Refactoring error
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Commits on Jul 25, 2017

Simplified masking by distinguishing between a binary mask and a continuous template. Both are 3d (and made into 4d volumes where necessary)
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PEP error
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Updated to deal with changes in fmrisim
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Mask_brain wasn't working for mask self
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Commits on Jul 28, 2017

Added automatic mask thresholding. Added (default) option of exponential machine noise
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PEP errors
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Relaxed test constraint since it is sometimes inaccurate with this mask type
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Commits on Sep 21, 2017

Extensive update. Changed how noise is calculated, now it is focused around SNR and SFNR. Made stimfunction and signal function more useable and extensible. Added more documentation
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Merge branch 'master' into fmrisim_mean_mask
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PEP errors
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Merge branch 'fmrisim_mean_mask' of https://github.com/CameronTEllis/BrainIAK into fmrisim_mean_mask
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Commits on Sep 22, 2017

PEP errors
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Updated fmrisim to accept any specified hrf. Changed utils to deal with the new procedure for generating functions
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PEP error
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PEP error
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PEP Error
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Rounding error
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Dimension error
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Changed rounding procedure for Stimfunction
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More hacky fix
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Error
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Error
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Commits on Sep 24, 2017

Updated the export functions so as to support making both 3 column files and epoch files from stim functions
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PEP error
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PEP error
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Commits on Oct 5, 2017

Fixed error with gamma_hrf assuming the temporal resolution
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Commits on Oct 14, 2017

Improved the peak detection of the masking function
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PEP error
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Commits on Oct 15, 2017

Improved the calculation of SNR
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Commits on Oct 16, 2017

Simplified the calculation of SNR
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Commits on Oct 18, 2017

Updated how system noise is calculated to be more realistic. Improved the tests done for calc_noise
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PEP error
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PEP error
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Commits on Oct 19, 2017

PEP error
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PEP error
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Commits on Oct 21, 2017

Initial commit of fmrisim multivariate jupyter notebook
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Commits on Nov 9, 2017

Updated with comments from (fantastic) Chris and Mingbo
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PEP errors
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Updated documentation for example notebook
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Updated the code for Mingbo's comments
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Commits on Nov 10, 2017

Changed AR default
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Merge branch 'master' into fmrisim_mean_mask
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