0.0.8

Release Notes

This long overdue release concentrates on adding testing, and improving documentation. Major changes include:

• Generating workflow descriptions for each run
• Streamline circleCI workflow
• Reducing memory usage

Thanks to all listed contributors, as well as to many not listed here !

Changes

• [ENH] Adding monoexponential curve fit (#409) @dowdlelt
• Fit to each subset of echoes and fit to all data (not mean). (#8) @tsalo
• [ENH] Stop writing __meica_mix.1D (#406) @frodeaa
• docs: add benoitberanger as a contributor (#398) @allcontributors
• [ENH] --debug flag appear now in the help & documentation (#385) @benoitberanger
• MAINT: Update numpy and Python requirements (#397) @effigies
• [FIX][ENH][TST] Adds datetime logfile and removes it from outputs, fixes stream handling (#391) @jbteves
• [FIX][TST] Adds curl installation where needed (#390) @jbteves
• docs: add monicayao as a contributor (#389) @allcontributors
• [TST] Add smoke tests to io.py and viz.py (#380) @monicayao
• [TST] Additional smoke tests for stats.py (#386) @monicayao
• [TST] Additional smoke tests for utils.py (#377) @monicayao
• Update to sync (#4) @monicayao
• [DOC] Allows small doc patches (#374) @jbteves
• [DOC] Update CONTRIBUTING and README with developer installation, contributing and testing instructions (#375) @jsheunis
• docs: add jsheunis as a contributor (#381) @allcontributors
• Sync new changes (#6) @dowdlelt
• [TST] New smoke tests for functions in decay.py (#367) @monicayao
• Update #3 (#3) @monicayao
• [FIX, TST] Fix CodeCov report upload (#371) @tsalo
• [TST] Streamline CircleCI workflow (#368) @tsalo
• [DOC] Fix links and sizes in approach documentation (#369) @tsalo
• [DOC] Update to automatically update copyright year (#366) @monicayao
• Update (#2) @monicayao
• [FIX] Use PCA-based variance explained in PCA decision tree (#364) @tsalo
• [DOC, ENH] Generate workflow description for each run (#349) @tsalo
• [DOC] Walk through TE-dependence in more detail (#354) @tsalo
• [ENH, REF] Reduce memory requirements for metric calculation and PCA (#345) @tsalo
• [doc] Add poster from OHBM 2019 meeting, fix RTD (#340) @emdupre
• Multi-echo background documentation edits (#351) @handwerkerd
• [DOC] Fix small typos in multi-echo.rst documentation (#348) @jsheunis
• update (#1) @monicayao
• [DOC] Add newsletter to README file & RTD homepage (#342) @KirstieJane
• [FIX] Add TR checking and user option (#333) @jbteves
• [DOC] Adding recommendations into multi-echo.rst (#341) @handwerkerd
• [DOC] Clean up approach page (#337) @tsalo
• [DOC] Corrects doc after refactor (#324) @jbteves
• [REF] Gets rid of mask argument in tedana.fit.dependence_metrics (#326) @jbteves
• [FIX] Modifies three-echo dataset url to new location (#329) @jbteves
• [REF] Changes model module -> metrics module (#325) @jbteves
• docs: add tsalo as a contributor (#323) @allcontributors
• docs: add tsalo as a contributor (#322) @allcontributors
• [DOC] Updates CONTRIBUTING to reflect contribution spec and bot (#309) @jbteves
• docs: add tsalo as a contributor (#321) @allcontributors
• docs: add monicayao as a contributor (#319) @allcontributors
• [DOC] Addition to the multi-echo fMRI section to include more background (#314) @monicayao
• [DOC] Update homepage > "about tedana" to redirect readers to relevant page (#313) @monicayao
• [DOC] Adds 'quick start' guidelines for new contributors (#293) @jbteves
• [DOC] Requests no Draft PRs in CONTRIBUTING (#296) @jbteves
• [DOC] Update Visual Reports Documentation (#311) @dowdlelt
• [FIX] Add early escape from TEDICA decision tree (#298) @tsalo
• update fork (#5) @dowdlelt
• docs: add emdupre as a contributor (#307) @allcontributors
• docs: add javiergcas as a contributor (#306) @allcontributors
• docs: add prantikk as a contributor (#305) @allcontributors
• docs: add rmarkello as a contributor (#304) @allcontributors
• docs: add dowdlelt as a contributor (#303) @allcontributors
• docs: add handwerkerd as a contributor (#302) @allcontributors
• docs: add tsalo as a contributor (#301) @allcontributors
• docs: add KirstieJane as a contributor (#300) @allcontributors
• docs: add jbteves as a contributor (#299) @allcontributors
• [REF] Create new stats module (#273) @tsalo
• [FIX] Sort comptable by varex before identifying outlier components (#295) @tsalo
• [REF] Reorganize selcomps and fitmodels_direct (#266) @tsalo
• [DOC] Updates copyright year (#291) @jbteves
• [ENH] Adds static logging filename (#280) @jbteves
• [DOC] Add Paused label description to CONTRIBUTING (#278) @jbteves
• [DOC] Adds information on why we use multi-echo (#288) @emdupre
• [DOC] Changes source->conda for env (de)activate (#286) @jbteves
• [DOC] Add stale issue policy to CONTRIBUTING (#279) @jbteves
• Update multi-echo.rst (#284) @handwerkerd
• [DOC] Fixes Random Seed Help Text (#281) @jbteves
• [REF, DOC] Document and refactor selcomps (#262) @tsalo
• [ENH] Improve manual component selection (#263) @tsalo
• [REF] Split eigendecomp into ICA and PCA files (#265) @tsalo

0.0.7

Release Notes

This release concentrates on improving performance and interpretability of tedana processing. Major changes include:

• Add options to control ICA attempts
• Implement automatric masking when no explicit masking provided
• Initial visual reports
• Speed up cluster-extent thresholding

Thanks to all listed contributors, as well as to many not listed here (@jbteves @handwerkerd @javiergcas) !

Changes

• [STY] Consolidate linter settings and ignore some style warnings (#216) @tsalo
• [ENH] Limit tedana to one core (#215) @tsalo
• [ENH] Add options to control ICA attempts (#224) @tsalo
• [REF] Clean up outdated/unused functions (#227) @tsalo
• [ENH] Automatically use Nilearn's EPI mask when no explicit mask is provided (#226) @tsalo
• [ENH] Adding simple figure output (#208) @dowdlelt
• [FIX] Normalize PCA mixing matrix over time, not component (#228) @tsalo
• [FIX] Remove WVPCA support (#233) @tsalo
• [FIX] scatter plot labeling issue. (#235) @dowdlelt
• [ENH] Update Figure Generation Code (#236) @dowdlelt
• [FIX, DOC] Use countnoise in decision table within selcomps (#238) @tsalo
• [REF] Add gscontrol module (#240) @tsalo
• [FIX] center component map at zero (#241) @dowdlelt
• [FIX] Make figures using un-orthogonalized mixing matrix (#246) @tsalo
• [REF] Clean up comptable handling in tedana.io (#242) @tsalo
• [ENH] Speed up cluster-extent thresholding function (#239) @tsalo
• [FIX] Fix use of d_table_score (#260) @tsalo
• [REF, DOC] Document PAID combination method (#264) @tsalo
• [DOC] Add dev calls to contributing guidelines (#271) @KirstieJane

0.0.6

Release Notes

We had several major changes this release, including:

• Changes PCA default component selection to MLE, with previous decision tree accessible through kundu_pca argument
• Adds verbose outputs for visualization and debugging
• Addition of tedort argument
• Bug fix for user-defined mask with poor signal

Improved documentation, logging, and issue templates also added.

With thanks to @dowdlelt, @jbteves, @katrinleinweber, @KirstieJane, and @tsalo !

Changes

• Hyperlink DOIs to preferred resolver (#165) @katrinleinweber
• [REF] Replace hard-coded F-statistic thresholds with scipy.stats function call (#156) @tsalo
• [FIX] Include ignored components in ME-DN T1c time series (#125) @tsalo
• [REF] Remove unused arguments and simplify CLI (#163) @tsalo
• [DOC] Add FAQ and link to ME papers spreadsheet (#160) @tsalo
• [DOC] Improve logging (#167) @tsalo
• [FIX] Reduce user-defined mask when there is no good signal (#172) @tsalo
• [ENH] Add tedort argument to tedana workflow (#155) @tsalo
• [ENH] Split automatic dimensionality detection from decision tree in TEDPCA (#164) @tsalo
• [ENH] Add verbose outputs for pipeline walkthrough (#174) @tsalo
• [fix] update python version support in README (#182) @emdupre
• [DOC] Fix eimask logging, ste definitions in eigendecomp (#184) @dowdlelt
• [DOC] Fix arg parser (#195) @dowdlelt
• Fix broken link to code of conduct (#198) @KirstieJane
• [DOC] Add tedana development setup instructions (#197) @jbteves
• Corrects README.md to show correct conda and pip instructions (#205) @jbteves
• [FIX] Propagate TR to ref_image header (#207) @dowdlelt
• [FIX] Do not use minimum mask for OC data in tedpca (#204) @tsalo
• [ENH] Adds issue templates for bugs and discussions (#189) @jbteves
• [ENH] Normalize all the line endings (#191) @jbteves

0.0.5

Release Notes

Major changes: This release reverts to the 2.5 version selection criteria, and it also switches the ICA implementation from mdp to sklearn. It is also includes a major overhaul of the documentation.

With thanks to @frodeaa, @RupeshGoud, and @jbteves for contributrions !

Changes

• [DOC] Rearrange badges in README (#118) @tsalo
• [ENH] Linting, update imports (#4) @emdupre
• [FIX] Add quiet and debug options to t2smap (#123) @emdupre
• [DOC] Add Python version info (#126) @tsalo
• [FIX] Accept non-NIFTI files without complaining (#128) @rmarkello
• [FIX] Remove nifti requirement in selcomps() (#130) @rmarkello
• Inital commit of tedana package (#1) @emdupre
• [DOC] Update multi-echo.rst (#138) @RupeshGoud
• [FIX] Logging in tedana and t2smap (#143) @frodeaa
• [ENH] Track PCA and ICA component selection decisions (#122) @tsalo
• [DOC] Improve documentation for pipeline (#133) @tsalo
• Documentation update for installation and environments in miniconda (#142) @jbteves
• [DOC] Add Support page (#150) @tsalo
• [ENH] Rename modules (#136) @frodeaa
• [DOC] Update documentation for interacting with other pipelines (#134) @emdupre
• Merge in @rmarkello PR (#19) @emdupre
• [TST] Support Python 3.5 (#154) @tsalo
• [DOC] Request for Comments: Roadmap and Contributing (#151) @emdupre
• [ENH] update ICA to sklearn from mdp (#44) @emdupre
• [DOC] RST formatting fixes for roadmap, contributing (#157) @emdupre
• [ENH] Switch to Selcomps 2.5 (#119) @emdupre
• [FIX] Loop through volumes in FIT method (#158) @tsalo

0.0.5-rc2

Release Notes

Update licensing for zenodo integration

Changes

• [FIX] Update license and license fields (#117)

0.0.5-rc1

Release Notes

To patch for the zenodo release

Changes

• [FIX] Lint zenodo.json (#116)

0.0.4

Release Notes

With thanks to @chrisfilo and @oesteban for suggestions !

Changes

• [FIX] add extensions in fnames for filewrite (#92)
• [ENH, FIX] Add wavelet denoising and fix t2smap workflow (#90)
• [DOC] Better commenting for component selection algorithm in selcomps (#91)
• [DOC, REF] Add files generated to function docstrings (#94)
• [FIX] Remove hardcoded numbers of echoes. (#95)
• [DOC] Add resources to RTD site (#99)
• [REF] Merge CLI into workflows (#100)
• [TST] Update testing environment (#103)
• [DOC] Update docstring for fixed_seed to ref None option (#104)
• [ENH] Add mask argument to t2smap, tedana (#108)
• [DOC, REF] Refactor select_comps and add shape checks to several functions (#105)
• [DOC] Streamline release process, add checklist to RTD (#109)
• [FIX] Drop gifti support (#114)
• [FIX] Explicitly strip extensions (#115)

0.0.3

Release Notes

Release including hot fix for JSON serialize error.

Changes

[FIX] Hot fix for JSON serialize error

0.0.2

Release Notes

This release improves documentation and handling of individually supplied echos.

Changes

[FIX] Add fname to TED dirname
[FIX] Improve gii file handling
[FIX] Fixes path handling and reference image errors
[DOC] Add discussion of gitter room
[DOC] Remove docker reference in contributing
[DOC] Remove installation RTD

Initial tedana release

The first release for tedana. Building off scripts originally developed in the ME-ICA pipeline, tedana is a python package for performing TE-Dependent Analysis on multi-echo fMRI data.

doi: 10.5281/zenodo.1250562