Brainiak

==========================

Features
--------

- matnormal: New package for matrix-normal models. (`341
<https://github.com/brainiak/brainiak/pull/341>`_)
- fmrisim: Add real-time generator. (`460
<https://github.com/brainiak/brainiak/pull/460>`_)
- isc: Add 'side' option to randomization tests. (`477
<https://github.com/brainiak/brainiak/pull/477>`_)
- reconstruct: Add 2D expansion to IEM module. (`482
<https://github.com/brainiak/brainiak/pull/482>`_)
- funcalign: Add save/load functionality to SRM. (`484
<https://github.com/brainiak/brainiak/pull/484>`_)

Bugfixes
--------

- isc: Fix pairwise bootstrap to tolerate NaNs. (`475
<https://github.com/brainiak/brainiak/pull/475>`_)

Documentation improvements
--------------------------

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

Deprecations and removals
-------------------------

- reconstruct: Rename IEM class. (`482
<https://github.com/brainiak/brainiak/pull/482>`_)
- Drop support for Python 3.5, which is no longer supported by NumPy. (`479
<https://github.com/brainiak/brainiak/pull/479>`_)

==========================

Features
--------

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


Documentation improvements
--------------------------

- Add ``--no-use-pep517`` Pip installation flag for compatibility with
Pip >= 19.1.1. (`454 <https://github.com/brainiak/brainiak/pull/454>`_)

===========================

Features
--------

- Added Conda packages for Python 3.7.

=========================

Features
--------

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

Deprecations and removals
-------------------------

- isfc: ISC/ISFC have a new API and are available in `brainiak.isc`, not
``brainiak.isfc``. (`384
<https://github.com/brainiak/brainiak/issues/384>`_)

=========================

Features
--------

- searchlight: Add ball shape. (`348
<https://github.com/brainiak/brainiak/pull/348>`_)
- eventseg: Added event_chains option and model_prior function. (`353
<https://github.com/brainiak/brainiak/pull/353>`_)
- srm: Added the ability to transform a new subject to a shared response.
(`371 <https://github.com/brainiak/brainiak/pull/371>`_).
- fmrisim: Added fitting procedure for SFNR and SNR parameters. Updated AR to
be ARMA, involving both the generation and estimation. (`372
<https://github.com/brainiak/brainiak/pull/372>`_)
- searchlight: Halved memory usage when ``pool_size=1``. (`386
<https://github.com/brainiak/brainiak/pull/386>`_)
- reprsimil: Added an option in BRSA to set the prior of SNR to be "equal"
across all voxels. (`387
<https://github.com/brainiak/brainiak/pull/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
<https://github.com/brainiak/brainiak/pull/372>`_).
- utils: Fix AFNI-style design matrix generation. (`381
<https://github.com/brainiak/brainiak/pull/381>`_)


Documentation improvements
--------------------------

- fcma: Clarify that image data is shuffled. (`365
<https://github.com/brainiak/brainiak/pull/365>`_)
- Fix Conda channels in install instructions. (`373
<https://github.com/brainiak/brainiak/pull/373>`_)


Deprecations and removals
-------------------------

- fmrisim: Removed plot_brain because other tools like nilearn do a much better
job at plotting data. (`372
<https://github.com/brainiak/brainiak/pull/372>`_)

===========================

Features
--------

- reprsimil: Changed the default optimizer of (G)BRSA to L-BFGD-B. (`337
<https://github.com/brainiak/brainiak/pull/337>`_)


Bugfixes
--------

- eventseg: Fixed bug that was causing fits to be asymmetric (`339
<https://github.com/brainiak/brainiak/issues/339>`_)


Documentation improvements
--------------------------

- reprsimil: Added explanation that both BRSA and GBRSA assume zero-mean in the
distribution of beta patterns. (`337
<https://github.com/brainiak/brainiak/pull/337>`_)