What’s new¶
0.4.0 (May 10, 2019)¶
This release produces effect, variance, statistic (t or F), Z-score, and p-value maps at every level, and enables smoothing at higher levels if preferred.
Additionally, documentation has been added at https://fitlins.readthedocs.io and versioning/packaging issues have been resolved.
FIX: Do not install FitLins as editable in Docker (https://github.com/poldracklab/fitlins/pull/137)
ENH: Save design matrix as TSV to output directory (https://github.com/poldracklab/fitlins/pull/143)
ENH: Enable smoothing at any analysis level (https://github.com/poldracklab/fitlins/pull/135)
ENH: Produce all available statistical maps from each analysis unit (https://github.com/poldracklab/fitlins/pull/131)
ENH: Add version to non-release Docker images. (https://github.com/poldracklab/fitlins/pull/136)
DOC: Flesh out documentation (https://github.com/poldracklab/fitlins/pull/147)
DOC: Build API docs on RTD (https://github.com/poldracklab/fitlins/pull/146)
DOC: Create Sphinx documentation with API autodocs (https://github.com/poldracklab/fitlins/pull/145)
MAINT: Drop Python 3.5 support (https://github.com/poldracklab/fitlins/pull/140)
CI: Run FitLins with coverage (https://github.com/poldracklab/fitlins/pull/144)
CI: Test FitLins on OpenNeuro DS000003, preprocessed with fMRIPrep 1.3.2 (https://github.com/poldracklab/fitlins/pull/141)
0.3.0 (April 19, 2019)¶
This release restores reports at the second level and higher, and enables isotropic smoothing with the nistats backend. Reporting has also been refactored to reduce clutter in the outputs.
With thanks to Karolina Finc, Rastko Ciric and Mathias Goncalves for contributions.
FIX: Restore level 2+ reports (https://github.com/poldracklab/fitlins/pull/130)
FIX: Remove uninformative metadata from derivative filenames (https://github.com/poldracklab/fitlins/pull/129)
FIX: Re-enable analysis level selection (https://github.com/poldracklab/fitlins/pull/120)
FIX: Switch plot colors to conventional blue for negative, red for positive (https://github.com/poldracklab/fitlins/pull/108)
ENH: Save crashfiles as text in working directory (https://github.com/poldracklab/fitlins/pull/121)
ENH: Add naive isotropic smoothing (https://github.com/poldracklab/fitlins/pull/104)
REF: Delegate isotropic smoothing to nistats (https://github.com/poldracklab/fitlins/pull/118)
DOC: Update README with latest help text, remove smoothing disclaimer (https://github.com/poldracklab/fitlins/pull/119)
MAINT: Add contributors to Zenodo (https://github.com/poldracklab/fitlins/pull/122)
MAINT: Consolidate configuration (https://github.com/poldracklab/fitlins/pull/113)
MAINT: Pybids 0.8 compatibility (https://github.com/poldracklab/fitlins/pull/109)
MAINT: Use numpy 1.15 to accommodate pytables (https://github.com/poldracklab/fitlins/pull/106)
0.2.0 (February 1, 2019)¶
This release marks a substantial refactoring in the wake of BIDS Derivatives RC1, fMRIPrep 1.2.x and pybids 0.7.0.
Reports at second level and higher are currently broken, but we’re at a point where neuroscout is depending on the current code base, the user base is increasing, and it’s worth having a starting point for considering new features.
With thanks to Alejandro de la Vega, Adina Wagner and Yaroslav Halchenko for contributions.
FIX: Allow derivatives to be a boolean value (https://github.com/poldracklab/fitlins/pull/91)
FIX: Restore report generation (https://github.com/poldracklab/fitlins/pull/88)
ENH: Plotting improvements (https://github.com/poldracklab/fitlins/pull/89)
ENH: Allow selecting for no space
--space ''option (https://github.com/poldracklab/fitlins/pull/96)ENH: Allow selecting for desc with
--descoption (https://github.com/poldracklab/fitlins/pull/95)MAINT: Depend on unreleased pybids commit (https://github.com/poldracklab/fitlins/pull/99)
MAINT: Pybids 0.7.0 compatibility (https://github.com/poldracklab/fitlins/pull/84)
0.1.0 (August 24, 2018)¶
This release moves FitLins to a Nipype workflow and provides a set of Nipype interfaces for interacting with BIDS Models and the nistats statistical package.
FIX: Correctly handle missing confounds (https://github.com/poldracklab/fitlins/pull/73)
ENH: Set loop_preproc during model loading (https://github.com/poldracklab/fitlins/pull/66)
REF: Second-level workflow (https://github.com/poldracklab/fitlins/pull/30)
DOC: Example model (https://github.com/poldracklab/fitlins/pull/63)
MAINT: Update nipype, grabbit and pybids dependencies (https://github.com/poldracklab/fitlins/pull/70)
0.0.6 (August 06, 2018)¶
Hotfix release.
FIX: Explicitly create working directory (https://github.com/poldracklab/fitlins/pull/61)
0.0.5 (August 01, 2018)¶
FIX: Limit NaN imputation and use mean non-zero value (https://github.com/poldracklab/fitlins/pull/57)
0.0.4 (July 05, 2018)¶
ENH: Allow models without non-HRF variables (https://github.com/poldracklab/fitlins/pull/55)
ENH: Make dataset_description optional (https://github.com/poldracklab/fitlins/pull/51)
ENH: Loop over preproc files, instead of raw BOLD files (https://github.com/poldracklab/fitlins/pull/50)
ENH: Add –n-cpus option to CLI (https://github.com/poldracklab/fitlins/pull/49)
ENH: Run datasinks on main thread (https://github.com/poldracklab/fitlins/pull/39)
ENH: Enable derivative label to tag pipelines (https://github.com/poldracklab/fitlins/pull/37)
ENH: Make dataset description (https://github.com/poldracklab/fitlins/pull/29)
ENH: Add trivial dataset_description.json (https://github.com/poldracklab/fitlins/pull/31)
ENH: Run auto model by default (https://github.com/poldracklab/fitlins/pull/26)
ENH: Rewrite first level analysis as Nipype workflow (https://github.com/poldracklab/fitlins/pull/16)
ENH: Add acq, rec, run and echo to output patterns (https://github.com/poldracklab/fitlins/pull/20)
FIX: Second level contrast computation, and dense/sparse transformation issues (https://github.com/poldracklab/fitlins/pull/48)
FIX: Include run in derivative names (https://github.com/poldracklab/fitlins/pull/43)
FIX: Force string input to snake_to_camel (https://github.com/poldracklab/fitlins/pull/41)
FIX: Versioneer adjustments (https://github.com/poldracklab/fitlins/pull/36)
FIX: Create group level results dir (https://github.com/poldracklab/fitlins/pull/22)
RF: Simplify entry-points, restore preproc discovery (https://github.com/poldracklab/fitlins/pull/38)
MAINT: Update pybids 0.6.3, grabbit 0.2.1 (https://github.com/poldracklab/fitlins/pull/52)
MAINT: Manage version with versioneer (https://github.com/poldracklab/fitlins/pull/35)
MAINT: Neuroscout changes / pybids updates (https://github.com/poldracklab/fitlins/pull/28)
MAINT: Add nipype dependency, remove unused code (https://github.com/poldracklab/fitlins/pull/27)
0.0.3 (March 9, 2018)¶
Maintenance release
Update grabbit (0.1.1), pybids (0.5.0) (#11)
Incorporate nistats/nistats#165 (#13)
Update Dockerfile, versioning (#14)
0.0.2 (March 5, 2018)¶
Hotfix, addressing deployment issues.
0.0.1 (March 5, 2018)¶
Initial release of FitLins, a BIDS-model fitting BIDS app.