Repository navigation

Fit parameters - #372

Merged

lcnature merged 54 commits into

brainiak:masterfrom

CameronTEllis:fit_parameters

Sep 2, 2018

Merged

Fit parameters#372
lcnature merged 54 commits into
brainiak:masterfrom
CameronTEllis:fit_parameters

Commits on Feb 4, 2018
- Added fitting procedure for sfnr and snr parameters
  CameronTEllis
  committed
  998705c
Commits on Feb 7, 2018
- Substantially reworked the noise estimation procedure in order to make it simpler and more tractable
  CameronTEllis
  committed
  2040c90
Commits on Feb 14, 2018
- Improved AR estimation and calculation
  CameronTEllis
  committed
  6361376
Commits on Feb 20, 2018
- Updated AR to be ARMA, involving both the generation and estimation
  CameronTEllis
  committed
  229f7bb
- Add statsmodels to 'setup.py'
  CameronTEllis
  committed
  3066c7a
Commits on Mar 8, 2018
- Added signal change function and update notebook script
  CameronTEllis
  committed
  8cf4fda
- Vectorized GRF calculation for 50x increase in speed (git add brainiak/utils/fmrisim.py)
  CameronTEllis
  committed
  c1d57f7
- Unintentional add
  CameronTEllis
  committed
  98e3877
Commits on Mar 9, 2018
- Did some iteration timing testing add added content
  CameronTEllis
  committed
  76209c8
- Tweaks of notebook and defaults in fmrisim
  CameronTEllis
  committed
  fda9f9e
Commits on Mar 12, 2018
- Improved the fitting procedure, especially for AR
  CameronTEllis
  committed
  4c3472c
Commits on Mar 14, 2018
- Updated how fitting is done and how machine noise is calculated
  CameronTEllis
  committed
  07d2425
- Updated how fitting is done and how machine noise is calculated
  CameronTEllis
  committed
  8388c07
- Updated how fitting is done and how machine noise is calculated
  CameronTEllis
  committed
  529b917
Commits on Mar 28, 2018
- Updated the export epoch file to deal with error in epoch number generation. Moreover, changed calc snr
  CameronTEllis
  committed
  4f82e48
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
  CameronTEllis
  committed
  0899cbd
Commits on May 16, 2018
- Fixed reference to noise dict before it wwas preset
  CameronTEllis
  committed
  8b071f3
Commits on May 24, 2018
- Increased the precision of the ar estimation and added a toggle in the noise dict for matching participants
  CameronTEllis
  committed
  2da8948
- Increased the precision of the ar estimation and added a toggle in the noise dict for matching participants
  CameronTEllis
  committed
  dc9cbe9
Commits on May 27, 2018
- Fit AR directly
  CameronTEllis
  committed
  f1f0bbe
Commits on May 28, 2018
- Consolidate spatial and temporal noise fitting
  CameronTEllis
  committed
  a543aac
- Adjusted noise terms
  CameronTEllis
  committed
  2ae082e
- Minor wording edits
  CameronTEllis
  committed
  9bbd190
- Increased test coverage for fitting
  CameronTEllis
  committed
  9a83a81
Commits on Jun 5, 2018
- Added a warning
  CameronTEllis
  committed
  20a9ac3
- Merge branch 'master' into fit_parameters
  CameronTEllis
  authored
  572244d
- PEP8
  CameronTEllis
  committed
  6ee9999
- PEP8
  CameronTEllis
  committed
  f9676c9
- PEP8
  CameronTEllis
  committed
  2a32b59
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
  CameronTEllis
  committed
  be7253d
- Substantial increase in coverage
  CameronTEllis
  committed
  2a1ca85
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
  CameronTEllis
  committed
  492f522
- PEP8
  CameronTEllis
  committed
  c15c2a4
- PEP8
  CameronTEllis
  committed
  e916a3d
- Cut iterations because you can't fit easily with different noise parameters
  CameronTEllis
  committed
  5d1193f
- PEP8
  CameronTEllis
  committed
  6dc19c9
- PEP8
  CameronTEllis
  committed
  557158b
- Fix the error
  CameronTEllis
  committed
  559da38
- Fix the error
  CameronTEllis
  committed
  fcb3d94
- Import class
  CameronTEllis
  committed
  8646b1a
Commits on Jun 8, 2018
- Fixed error exception
  CameronTEllis
  committed
  f0681e9
Commits on Jun 26, 2018
- Incorporated Mingbo's edits
  CameronTEllis
  committed
  98b9446
- Updated smoothing dimensions test
  CameronTEllis
  committed
  6e90c17
- Indent error
  CameronTEllis
  committed
  e52d0f0
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
  CameronTEllis
  committed
  2cf2581
Commits on Aug 10, 2018
- Corrected error in generating system noise. Specifically spatial noise was being double counted
  CameronTEllis
  committed
  f9c7ff1
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
  CameronTEllis
  committed
  ac1183b
Commits on Aug 18, 2018
- Removed the balancing of spatial_sd based on temporal_sd
  CameronTEllis
  committed
  7b8bf11
Commits on Aug 19, 2018
- Update test_fmrisim.py
  lcnature
  authored
  9e41edc
- Merge branch 'master' into fit_parameters
  lcnature
  authored
  1f61d02
Commits on Aug 31, 2018
- Merge branch 'master' into fit_parameters
  CameronTEllis
  authored
  d4fbd9b
Commits on Sep 2, 2018
- adding a check that `magnitude` is indeed a list
  lcnature
  authored
  d6e3959
- Update fmrisim.py
  lcnature
  authored
  657d54d
- Update fmrisim.py
  lcnature
  authored
  276bdfd

Commits

Commits on Feb 4, 2018

Commits on Feb 7, 2018

Commits on Feb 14, 2018

Commits on Feb 20, 2018

Commits on Mar 8, 2018

Commits on Mar 9, 2018

Commits on Mar 12, 2018

Commits on Mar 14, 2018

Commits on Mar 28, 2018

Commits on May 15, 2018

Commits on May 16, 2018

Commits on May 24, 2018

Commits on May 27, 2018

Commits on May 28, 2018

Commits on Jun 5, 2018

Commits on Jun 6, 2018

Commits on Jun 7, 2018

Commits on Jun 8, 2018

Commits on Jun 26, 2018

Commits on Jul 23, 2018

Commits on Aug 10, 2018

Commits on Aug 13, 2018

Commits on Aug 18, 2018

Commits on Aug 19, 2018

Commits on Aug 31, 2018

Commits on Sep 2, 2018