Fit parameters - #372

Merged

lcnature merged 54 commits into

brainiak:masterfrom

CameronTEllis:fit_parameters

Sep 2, 2018

Commits on Feb 4, 2018

Added fitting procedure for sfnr and snr parameters
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Commits on Feb 7, 2018

Substantially reworked the noise estimation procedure in order to make it simpler and more tractable
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Commits on Feb 14, 2018

Improved AR estimation and calculation
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Commits on Feb 20, 2018

Updated AR to be ARMA, involving both the generation and estimation
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Add statsmodels to 'setup.py'
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Commits on Mar 8, 2018

Added signal change function and update notebook script
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Vectorized GRF calculation for 50x increase in speed (git add brainiak/utils/fmrisim.py)
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Unintentional add
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Commits on Mar 9, 2018

Did some iteration timing testing add added content
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Tweaks of notebook and defaults in fmrisim
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Commits on Mar 12, 2018

Improved the fitting procedure, especially for AR
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Commits on Mar 14, 2018

Updated how fitting is done and how machine noise is calculated
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Updated how fitting is done and how machine noise is calculated
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Updated how fitting is done and how machine noise is calculated
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Commits on Mar 28, 2018

Updated the export epoch file to deal with error in epoch number generation. Moreover, changed calc snr
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Commits on May 15, 2018

Improved export_epoch, added more logging info, zscoring AR, reduced AR coefs to 1, added some warnings/tests of input data quality, split fitting up into 3 functions
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Commits on May 16, 2018

Fixed reference to noise dict before it wwas preset
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Commits on May 24, 2018

Commits on May 27, 2018

Fit AR directly
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Commits on May 28, 2018

Consolidate spatial and temporal noise fitting
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Adjusted noise terms
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Minor wording edits
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Increased test coverage for fitting
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Commits on Jun 5, 2018

Added a warning
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Merge branch 'master' into fit_parameters
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PEP8
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PEP8
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PEP8
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Commits on Jun 6, 2018

Removed plot_brain because other tools like nilearn do a much better job at plotting data. Minor edits and tweaks based on testing
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Substantial increase in coverage
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Commits on Jun 7, 2018

Removed plot_brain because other tools like nilearn do a much better job at plotting data. Minor edits and tweaks based on testing
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PEP8
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PEP8
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Cut iterations because you can't fit easily with different noise parameters
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PEP8
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PEP8
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Fix the error
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Fix the error
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Import class
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Commits on Jun 8, 2018

Fixed error exception
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Commits on Jun 26, 2018

Incorporated Mingbo's edits
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Updated smoothing dimensions test
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Indent error
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Commits on Jul 23, 2018

Changed the fitting procedure of _fit_spatial and _fit_temporal so that they are not made negative by default, added more description throughout
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Commits on Aug 10, 2018

Corrected error in generating system noise. Specifically spatial noise was being double counted
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Commits on Aug 13, 2018

Added documentation to clarify how nonbrain voxels affect SNR, how SNR is calculated and the importance of using unmasked data for generating templates
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Commits on Aug 18, 2018

Removed the balancing of spatial_sd based on temporal_sd
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Commits on Aug 19, 2018

Commits on Aug 31, 2018

Merge branch 'master' into fit_parameters
CameronTEllis
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Commits on Sep 2, 2018