Recent Releases of fitlins
fitlins - 0.11.0
Release Notes
New feature release in the 0.11.x series.
This version bump reflects changes that appear mostly in PyBIDS, including improved handling of intercept columns and variables from tabular metadata files like participants.tsv.
Changes
- MNT: Use latest coverage by @effigies in https://github.com/poldracklab/fitlins/pull/354
- MNT: Remove unused packages from docker image by @effigies in https://github.com/poldracklab/fitlins/pull/353
- Allow models with no name by @adelavega in https://github.com/poldracklab/fitlins/pull/357
- PIN pybids 0.15.1 by @adelavega in https://github.com/poldracklab/fitlins/pull/363
- RF: Fitlins output reorganization by @shashankbansal6 in https://github.com/poldracklab/fitlins/pull/355
- Build(deps): Bump docker/build-push-action from 2 to 3 by @dependabot in https://github.com/poldracklab/fitlins/pull/369
- Build(deps): Bump docker/login-action from 1 to 2 by @dependabot in https://github.com/poldracklab/fitlins/pull/370
- Build(deps): Bump docker/setup-buildx-action from 1 to 2 by @dependabot in https://github.com/poldracklab/fitlins/pull/368
- Build(deps): Bump actions/setup-python from 3 to 4 by @dependabot in https://github.com/poldracklab/fitlins/pull/372
- add github source links by @Shotgunosine in https://github.com/poldracklab/fitlins/pull/376
- Adding a section on estimators by @Shotgunosine in https://github.com/poldracklab/fitlins/pull/375
- DOC: Link out to BIDS Stats Models docs instead of maintaining our own by @Shotgunosine in https://github.com/poldracklab/fitlins/pull/378
- CI: Add a build to test with unreleased pybids by @effigies in https://github.com/poldracklab/fitlins/pull/386
- FIX: Handle correct contrasts and intercepts being passed from PyBIDS by @effigies in https://github.com/poldracklab/fitlins/pull/387
Full Changelog: https://github.com/poldracklab/fitlins/compare/0.10.1...0.11.0
- Python
Published by effigies over 3 years ago
fitlins - 0.10.1
Release notes
Bug-fix release in the 0.10.x series.
Most of the fixes come in the upstream fixes of PyBIDS, which will get bundled in the Docker image.
Changes
- ENH: Set prog name to fitlins, regardless of which CLI program was called (https://github.com/poldracklab/fitlins/pull/350)
- MNT: Update
bug_report.md(https://github.com/poldracklab/fitlins/pull/337) - CI: Comprehensive testing (https://github.com/poldracklab/fitlins/pull/344)
- CI: Unify Docker deployment steps (https://github.com/poldracklab/fitlins/pull/334)
- Build(deps): Bump actions/cache from 2 to 3 (https://github.com/poldracklab/fitlins/pull/347)
- Build(deps): Bump actions/checkout from 2 to 3 (https://github.com/poldracklab/fitlins/pull/343)
- Build(deps): Bump actions/setup-python from 2 to 3 (https://github.com/poldracklab/fitlins/pull/340)
Full Changelog: https://github.com/poldracklab/fitlins/compare/0.10.0...0.10.1
- Python
Published by effigies about 4 years ago
fitlins - 0.10.0
Release Notes
New feature release in the 0.10.x series.
This release implements support for BIDS Stats Models 1.0.0-rc1. While we have attempted not to break old-style models, we no longer support them.
What's Changed
- Temporarily pull pybids from github maintenance branch by @adelavega in https://github.com/poldracklab/fitlins/pull/308
- Fix version info & detail activating venv on different OS by @complexbrains in https://github.com/poldracklab/fitlins/pull/311
- FIX: Minor fixes by @effigies in https://github.com/poldracklab/fitlins/pull/326
- RF: Use the new bids stats model by @shashankbansal6 in https://github.com/poldracklab/fitlins/pull/298
- DOC: Update example models by @effigies in https://github.com/poldracklab/fitlins/pull/294
- Review PR for #298 by @effigies in https://github.com/poldracklab/fitlins/pull/314
- STY: Reformat to black, address flake8 issues by @shashankbansal6 in https://github.com/poldracklab/fitlins/pull/316
- FIX: minor typo; missed restyling in afni.py by @shashankbansal6 in https://github.com/poldracklab/fitlins/pull/328
- ENH: Migrate CircleCI to github actions by @shashankbansal6 in https://github.com/poldracklab/fitlins/pull/329
- CI: Check for secrets before deploying, switch to python-build by @effigies in https://github.com/poldracklab/fitlins/pull/332
- CI: Update ds003 tests by @effigies in https://github.com/poldracklab/fitlins/pull/331
New Contributors
- @complexbrains made their first contribution in https://github.com/poldracklab/fitlins/pull/311
- @shashankbansal6 made their first contribution in https://github.com/poldracklab/fitlins/pull/298
Full Changelog: https://github.com/poldracklab/fitlins/compare/0.9.2...0.10.0
- Python
Published by effigies over 4 years ago
fitlins - 0.9.0
Release Notes
New feature release in the 0.9.x series.
CHANGES
This release added AFNI's 3dREMLfit for first-level estimation, dropped nistats in favor of nilearn.stats, added test reference outputs, among other minor improvements.
- FIX: AFNI TSNR calculation, ADD: BlurToFWHM, ADD: testing outputs against reference (https://github.com/poldracklab/fitlins/pull/280) *
- FIX: AFNI contrast bool (https://github.com/poldracklab/fitlins/pull/266)
- ENH: Writeout estimator to derivative description (https://github.com/poldracklab/fitlins/pull/278)
- ENH: disable automatic drift modeling (https://github.com/poldracklab/fitlins/pull/276)
- ENH: modify path patterns to make task optional (https://github.com/poldracklab/fitlins/pull/275)
- ENH: Add AFNI 3dREMLfit for first-level estimation (https://github.com/poldracklab/fitlins/pull/171)
- TST: Add dummy dataset for pytest/local testing (https://github.com/poldracklab/fitlins/pull/262)
- MNT: Update PyBIDS and nilearn (https://github.com/poldracklab/fitlins/pull/268)
- CI: Make faster? (https://github.com/poldracklab/fitlins/pull/264)
- Python
Published by release-drafter[bot] over 5 years ago
fitlins - 0.8.0
Release Notes
New feature release in the 0.8.x series.
This release includes a change where events that are not explicitly convolved are modeled with boxcar functions instead of the nistats default.
CHANGES
- FIX: Sparse matrix should be in long format, and HRF should be None by default (#259)
- Python
Published by effigies over 5 years ago
fitlins - 0.7.0
Release Notes
New feature release in the 0.7.x series. This is an accumulation of changes over several months.
This release requires PyBIDS 0.12 and includes some quite provisional CIFTI-2 support as well as log-likelihood and R^2 maps for assessing goodness of fit.
CHANGES
- FIX: Downgrade Sphinx to <3.0 (https://github.com/poldracklab/fitlins/pull/226)
- FIX: Validate BIDS datasets except when searching for models (https://github.com/poldracklab/fitlins/pull/214)
- FIX: Blacklist coverage >=5 (https://github.com/poldracklab/fitlins/pull/209)
- ENH: Bundle Conte69 surfaces (https://github.com/poldracklab/fitlins/pull/249)
- ENH: Add CIFTI-2 support (https://github.com/poldracklab/fitlins/pull/239)
- ENH: Add logL as model output (https://github.com/poldracklab/fitlins/pull/230)
- ENH: Save model level output (r-squared) (https://github.com/poldracklab/fitlins/pull/224)
- ENH: Add FEMA as key value to stat
path_pattern(https://github.com/poldracklab/fitlins/pull/220) - RF: Accept nipype configurations from users (https://github.com/poldracklab/fitlins/pull/229)
- MNT: Update requirements (https://github.com/poldracklab/fitlins/pull/225)
- MNT: Bump pybids to 0.10.2 (https://github.com/poldracklab/fitlins/pull/216)
- CI: Improve outputs (https://github.com/poldracklab/fitlins/pull/218)
- Python
Published by effigies almost 6 years ago
fitlins - 0.6.0
Release Notes
New feature release in the 0.6.x series.
This release respects recent changes to the BIDS-StatsModels draft specification to support fixed-effects meta-analysis (FEMA) contrasts, and renames "AutoContrasts" to "DummyContrasts".
Provisional support for F-tests has been added.
Additional rearchitecting by Dylan Nielson provides significant speedups for large datasets by caching BIDS layout information.
CHANGES
- SPEC: Add fixed effects (FEMA) contrasts (https://github.com/poldracklab/fitlins/pull/191)
- SPEC: Change AutoContrasts to DummyContrasts (https://github.com/poldracklab/fitlins/pull/197)
- FIX: Don't pass ignore and force index to
init_fitlins_wf(https://github.com/poldracklab/fitlins/pull/202) - FIX: BIDSelect confusion between Nifti and JSON (https://github.com/poldracklab/fitlins/pull/193)
- FIX: Set
smoothing_fwhmafter creating next level. (https://github.com/poldracklab/fitlins/pull/190) - FIX: Recognize cosine columns without underscores (https://github.com/poldracklab/fitlins/pull/185)
- ENH: Update logging levels (https://github.com/poldracklab/fitlins/pull/198)
- ENH: Add option to load BIDS layouts from database file (https://github.com/poldracklab/fitlins/pull/187)
- ENH: Add memory estimate for first-level models, enable memory management (https://github.com/poldracklab/fitlins/pull/199)
- ENH: Avoid casting BOLD data to float64 if possible (https://github.com/poldracklab/fitlins/pull/196)
- ENH: Add F-tests (https://github.com/poldracklab/fitlins/pull/195)
- ENH: Drop missing model inputs (https://github.com/poldracklab/fitlins/pull/183)
- RF: Abstract interfaces to simplify swappability (https://github.com/poldracklab/fitlins/pull/188)
- Python
Published by effigies over 6 years ago
fitlins - 0.5.0
Release Notes
This release features significant improvements to reporting and documentation, including a Jupyter notebook to demonstrate usage. Example models are now in the main branch of the repository, and annotated in the documentation.
CHANGES
- FIX: Smoothing level, check length (https://github.com/poldracklab/fitlins/pull/157)
- FIX: mask parameter to FirstLevelModel is deprecated for mask_img (https://github.com/poldracklab/fitlins/pull/158)
- ENH: Add ds000117 model (https://github.com/poldracklab/fitlins/pull/163)
- ENH: Move to single-page report (https://github.com/poldracklab/fitlins/pull/161)
- ENH: Add task-vs-baseline contrast to ds003 (https://github.com/poldracklab/fitlins/pull/160)
- ENH: Reporting cleanups (https://github.com/poldracklab/fitlins/pull/155)
- DOC: Curate reports and models (https://github.com/poldracklab/fitlins/pull/153)
- DOC: Add example running through DS003 (https://github.com/poldracklab/fitlins/pull/152)
- MAINT: BIDSLayout.get() parameter "extensions" deprecated (https://github.com/poldracklab/fitlins/pull/167)
- MAINT: Update pybids dependency, package name (https://github.com/poldracklab/fitlins/pull/166)
- Python
Published by effigies almost 7 years ago
fitlins - 0.4.0
Release Notes
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.
CHANGELOG
- 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)
- Python
Published by effigies about 7 years ago
fitlins - 0.3.0
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)
- Python
Published by effigies about 7 years ago
fitlins - 0.2.0
Release Notes
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.
CHANGES
- 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)
- Python
Published by effigies over 7 years ago
fitlins - 0.1.0
Release Notes
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.
CHANGES
- 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)
- Python
Published by release-drafter[bot] almost 8 years ago
fitlins - 0.0.4
With thanks to Alejandro De La Vega for many contributions.
Changelog
- 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 snaketocamel (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)
- Python
Published by effigies almost 8 years ago
fitlins - 0.0.1
Initial release of FitLins, a BIDS-model fitting BIDS app.
FitLins uses PyBIDS and Nistats to fit general linear models. It is designed to use preprocessed functional series conforming to the draft BIDS Derivatives specification, and in particular has been tested on FMRIPREP-preprocessed datasets.
- Python
Published by effigies over 8 years ago