Release notes¶

BrainIAK 0.11 (2020-10-14)¶

Features¶

matnormal: New package for matrix-normal models. (#341)
fmrisim: Add real-time generator. (#460)
isc: Add ‘side’ option to randomization tests. (#477)
reconstruct: Add 2D expansion to IEM module. (#482)
funcalign: Add save/load functionality to SRM. (#484)

Bugfixes¶

isc: Fix pairwise bootstrap to tolerate NaNs. (#475)

Documentation improvements¶

fmrisim: Add details for noise_dict. (#474)
isc: Update permutation doc to clarify pairwise groups. (#476)
isc: Add caveats about false positive rates. (#480)
Remove --no-use-pep517 Pip installation flag, superfluous with Pip >= 20.2 (#479)

Deprecations and removals¶

reconstruct: Rename IEM class. (#482)
Drop support for Python 3.5, which is no longer supported by NumPy. (#479)

BrainIAK 0.10 (2020-02-06)¶

Features¶

reconstruct: Add inverted encoding model (IEM) for recreating continuous representations in new package for reconstruction methods. (#364)
funcalign: Add FastSRM module for input data that does not fit in RAM. (#421)
fmrisim: Update to how drift is calculated and used. (#437)
searchlight: Allow processing single voxels. (#440)
eventseg: Add split-merge feature to improve fits when event lengths are highly uneven. (#451)

Documentation improvements¶

Add --no-use-pep517 Pip installation flag for compatibility with Pip >= 19.1.1. (#454)

BrainIAK 0.9.1 (2019-08-27)¶

Features¶

Added Conda packages for Python 3.7.

BrainIAK 0.9 (2019-06-18)¶

Features¶

isc: Revamped ISC/ISFC functionality with more statistical tests. (#384)
utils: phase_randomize outputs phase-scrambled input data, not tied to ISC/ISFC. (#396)
utils: p_from_null no longer estimates distribution, simply returns p-value. (#397)
isc: Analyses will now tolerate NaNs or tolerate a proportion of NaNs. (#398)
isc: Output either vectorized triangle and diagonal or square matrices. (#399)
isc: Asymmetric ISFC analysis can now be performed based on a targets array. (#409)
Added tutorials to Docker image. (#425)

Deprecations and removals¶

isfc: ISC/ISFC have a new API and are available in brainiak.isc, not brainiak.isfc. (#384)

BrainIAK 0.8 (2018-11-06)¶

Features¶

searchlight: Add ball shape. (#348)
eventseg: Added event_chains option and model_prior function. (#353)
srm: Added the ability to transform a new subject to a shared response. (#371).
fmrisim: Added fitting procedure for SFNR and SNR parameters. Updated AR to be ARMA, involving both the generation and estimation. (#372)
searchlight: Halved memory usage when pool_size=1. (#386)
reprsimil: Added an option in BRSA to set the prior of SNR to be “equal” across all voxels. (#387)

Bugfixes¶

fmrisim: Corrected error in generating system noise; specifically spatial noise was being double counted. Updated the export epoch file to deal with error in epoch number generation. (#372).
utils: Fix AFNI-style design matrix generation. (#381)

Documentation improvements¶

fcma: Clarify that image data is shuffled. (#365)
Fix Conda channels in install instructions. (#373)

Deprecations and removals¶

fmrisim: Removed plot_brain because other tools like nilearn do a much better job at plotting data. (#372)

BrainIAK 0.7.1 (2018-02-20)¶

Features¶

reprsimil: Changed the default optimizer of (G)BRSA to L-BFGD-B. (#337)

Bugfixes¶

eventseg: Fixed bug that was causing fits to be asymmetric (#339)

Documentation improvements¶

reprsimil: Added explanation that both BRSA and GBRSA assume zero-mean in the distribution of beta patterns. (#337)

BrainIAK 0.7 (2018-02-12)¶

Features¶

funcalign: Added the Robust Shared Response Model method. (#302)
fmrisim: Update convolution and drift. (#309)
eventseg: Added option to compute p values for ISC and ISFC (#310)
Added Conda packages. (#328)

Documentation improvements¶

Updated the searchlight API docs. (#324)

BrainIAK 0.6 (2017-11-10)¶

Features¶

reprsimil: Add Group Bayesian RSA, add transform (decoding) and score (model selection) functions, add automatic determination of the number of necessary nuisance regressors. utils: modified gen_design to make the generated design matrix approximately scaled in amplitudes. (#194)
searchlight: Improved performance via tweaked multiprocessing usage. (#240)
fmrisim: Updated drift calculation and masking. (#244)
eventseg: Add set_event_patterns() and notebook example (#266)
Added a Docker image for testing BrainIAK without installing. (#272)
eventseg: Fixed numerical instability bug, added utility function for weighted variance (#292)
Restricted multiprocessing to the available number of CPUs. (#293)

Bugfixes¶

searchlight: Do not use sys.exit. (#156)
reprsimil: Follow random number guidelines. (#239)

Deprecations and removals¶

Changed GitHub organization to BrainIAK. Update your remote URLs. (#277)

BrainIAK 0.5 (2017-05-23)¶

Features¶

FCMA partial similarity matrix option. (#168)
Faster FCMA cross validation via multiprocessing. (#176)
Inter-subject correlation (ISC) and inter-subject functional correlation (ISFC). (#183)
Input/output and image modules with high-level APIs. (#209)
FCMA support for random permutations. (#217)
A distributed version of SRM. (#220)
Shape masks for the searchlight. (#221)

Deprecations and removals¶

Changed fmrisim to compute signal-to-fluctuation-noise ratio (SFNR) instead of signal-to-noise ratio (SNR). (#224)

BrainIAK 0.4 (2017-01-19)¶

Features¶

Distributed searchlight. (#148)
Multi-voxel pattern analysis (MVPA) support in FCMA. (#154, #157)
Fast Pearson correlation coefficient computation. (#159)

BrainIAK 0.3.2 (2016-10-31)¶

Features¶

Faster event segmentation via Cython implementation. (#111)
fMRI data simulator (fmrisim). (#135)

BrainIAK 0.3.1 (2016-09-30)¶

Features¶

Event segmentation. (#72)
Full correlation matrix analysis (FCMA). (#97, #122)
Bayesian representational similarity analysis (BRSA). (#98)
Deterministic SRM. (#102)
Semi-supervised shared response model (SSSRM). (#108)

BrainIAK 0.3 (2016-09-30) [YANKED]¶

BrainIAK 0.2 (2016-08-03)¶

Features¶

Hyperparameter optimization. (#58)

Deprecations and removals¶

Removed _ from package names. (#73)

BrainIAK 0.1 (2016-07-12)¶

Features¶

Initial release, including:
- Shared response model (SRM).
- Topographic factor analysis (TFA) and hierarchical topographical factor analysis (HTFA).