{ "info": { "author": "James Kent", "author_email": "james-kent@uiowa.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 1 - Planning", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX", "Operating System :: Unix", "Programming Language :: Python", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Utilities" ], "description": ".. _readme:\n\n============\nNiBetaSeries\n============\n\nIf you are viewing this file on GitHub, please see our\n`readthedocs page `_\nfor links to render properly.\n\n\n\nWhat is NiBetaSeries?\n---------------------\nNiBetaSeries is BIDS_-compatible `application `_\nthat calculates betaseries correlations.\nIn brief, a beta coefficient (i.e., parameter estimate) is calculated\nfor each trial (or event) resulting in a series of betas (\"betaseries\")\nthat can be correlated across regions of interest.\n\nWhy should I use it?\n--------------------\nThere are potential insights hidden in your task fMRI data.\nRest fMRI enjoys a multitude of toolboxes which can be applied to task fMRI\nwith some effort, but there are not many toolboxes that focus on making\nbetaseries.\nBetaseries can then be used for correlations/classifications and\na multitude of other analyses.\nWhile a couple alternatives exist (pybetaseries_ and BASCO_), NiBetaSeries\nis the only application to interface with BIDS_ organized data with the goal\nof providing a command-line application experience like fMRIPrep_.\n\nWhat does NiBetaSeries give me?\n-------------------------------\nCurrently NiBetaSeries returns the beta series images and optionally\nsymmetric z-transformed correlation matrices with an entry for each\nparcel defined in the atlas.\n\n.. note:: The betas (i.e., parameter estimates) are generated using either\n the \"Least Squares Separate\" or \"Least Squares All\" procedures.\n Please read the betaseries page for more background information.\n\nWhat do I need to run NiBetaSeries?\n-----------------------------------\nNiBetaSeries takes BIDS_ and preprocessed data as input that satisfy the\n`BIDS derivatives specification `_.\nIn practical terms, NiBetaSeries uses the output of fMRIPrep_,\na great BIDS-compatible preprocessing tool.\nNiBetaSeries requires the input and the atlas to already\nbe in the same space (e.g., MNI space).\nFor more details, see usage and the tutorial\n(sphx_glr_auto_examples_plot_run_nibetaseries.py)\n\nGet Involved\n------------\nThis is a very young project that still needs some tender loving care to grow.\nThat's where you fit in!\nIf you would like to contribute, please read our code_of_conduct\nand contributing page (contributing).\n\nThanks!\n-------\nThis project heavily leverages `nipype `_,\n`nilearn `_, `pybids `_, and\n`nistats `_ for development.\nPlease check out their pages and support the developers.\n\n.. _BASCO: https://www.nitrc.org/projects/basco/\n.. _pybetaseries: https://github.com/poldrack/pybetaseries\n.. _BIDS: http://bids.neuroimaging.io/\n.. _fMRIPrep: http://fmriprep.readthedocs.io/en/latest/\n\n.. _changelog:\n\n=========\nCHANGELOG\n=========\n\n0.4.0 (October 07, 2019)\n------------------------\nThis has been a busy month for NiBetaSeries.\nWe have two more methods for calculating betas (LSA and FS),\nand LSS has been modified to account for separate conditions.\nAll of this great work is thanks to @tsalo.\n\nThe second major change is the refactor of how we read from\nthe FMRIPREP directory, previously we assumed results from\nfmriprep version (< v1.2.0), but now we only support files output\nfrom fmriprep (>= v1.2.0).\nIf you have results from an older version of fmriprep, check our\nFAQ for a potential solution.\n\nThe third major change is the generation of a citation template,\nso you can easily populate your methods section with the appropriate information.\nAgain, thanks to @tsalo for this marvelous contribution.\n\nThe fourth and final major change (in no particular order), is passing the\nbeta series image maps directly to the output directory, no longer requiring the\nuser to have an atlas and a lookup table to use NiBetaSeries.\nThis will allow users to use the beta series image maps for whatever downstream\nanalysis they wish.\n\nThank you to all the contributors mentioned below for improving NiBetaSeries\nthrough documentation fixes and other code changes.\n\nAn unsung hero is @PeerHerholz for code review and\nbeneficial recommendations for the future of NiBetaSeries, Thank you!\nAlso not listed is @mwvoss for opening issue #123.\nMaking a good issue is work and should be recognized, thank you!\n\nWhile I have almost certainly missed giving thanks to everyone that\nhas helped, please know I appreciate your contributions and I'm\nthankful you took some time out of your day to help this project grow.\n\n* [DOC] update instructions with template checklist (#242) @jdkent\n* [FIX] update code-server version (#238) @jdkent\n* [DOC] Generate citable boilerplates for workflows (#205) @tsalo\n* [DOC] Clarify in demo that you are stripping color codes #123 (#234) @ipacheco-uy\n* [DOC] Fix documentation headers (#235) @atrievel\n* [FIX] add nano to dev container (#233) @pranesh-sp\n* [DOC] add lsa section (#231) @jdkent\n* [DOC] add joss badge (#229) @zkhan12\n* [ENH,DOC] add development documentation section (#222) @jdkent\n* [DOC,FIX] add fake img and lut to participant workflow (#225) @jdkent\n* [ENH] Implement finite BOLD response- separate (FS) modeling (#204) @tsalo\n* [MAINT] allow more lenience for pull requests (#223) @jdkent\n* [ENH] Make atlases optional (#213) @jdkent\n* [FIX,DOC] make title for changelog (#221) @jdkent\n* [MAINT] make travisci more efficient (#216) @jdkent\n* [FIX] make codecov yaml valid (#220) @jdkent\n* [FIX] show binder badge on readthedocs (#219) @jdkent\n* [ENH,DOC] sphinx gallery binder (#217) @jdkent\n* [MAINT] make codecov more lenient (#215) @jdkent\n* [FIX] use scope=derivatives in collect_data (#212) @jdkent\n* [FIX] respond to suggested edits (#206) @jdkent\n* [ENH] Implement least squares- all (LSA) modeling (#202) @tsalo\n* [TST] add more tests (#201) @jdkent\n* [FIX, DOC] Rename low-pass filter to high-pass filter (#198) @tsalo\n* [MAINT] explicitly set codecov settings (#200) @jdkent\n* [ENH,FIX] refactor bids file processing (#193) @jdkent\n* [ENH] Separate other conditions in LSS model (#191) @tsalo\n\n\n0.3.2 (September 04, 2019)\n--------------------------\n\nThis release is special because it will be published in the\nJournal of Open Source Software (JOSS).\nOne condition of this is that the authors on the paper be the only authors in the zenodo file.\nI will modify the authors listed on the zenodo file for this release,\nbut I will add all contributors back on for the subsequent release.\n\n* [MAINT] fix zenodo file\n\n0.3.1 (September 04, 2019)\n--------------------------\n\nChanges to installation and documentation, but no functional code changes.\n\n* [DOC] address review comments (#185) @jdkent\n* [DOC] add everyone to contributors in the zenodo file (#188) @jdkent\n* [MAINT] Change Installation Method (#187) @jdkent\n* [ENH] add code server (#182) @jdkent\n* [MAINT] build tags (#183) @jdkent\n\n0.3.0 (August 29, 2019)\n-----------------------\n\nThanks to @PeerHerholz and @njvack for their contributions on this release.\nSpecial thanks to @snastase for being a great reviewer and improving the project\noverall.\n\n* [ENH] reduce focus on parcellations (#179) @jdkent\n* [FIX] generalized -> general linear model description (#178) @jdkent\n* [DOC] Add math (#177) @jdkent\n* [FIX] remove .git from the binder url (#175) @jdkent\n* [FIX] add pypiwin32 as conditional dependency (#173) @jdkent\n* [FIX] add readthedocs config file (#174) @jdkent\n* [DOC] Minor changes to documentation text (#163) @snastase\n* [MAINT] fix tagging/pushing docker images (#160) @jdkent\n* [FIX] binder ci triggers (#159) @jdkent\n* [ENH] add binder (#158) @jdkent\n* [MAINT] Change Install Strategy (#157) @jdkent\n* [DOC] Clarify Documentation (#156) @jdkent\n* [FIX] Only hyphens for commandline parameters (#155) @jdkent\n* [DOC] add concrete example of nibs (#154) @jdkent\n* [DOC] add references (#153) @jdkent\n* [MAINT] build docs on circleci (#152) @jdkent\n* [MAINT] temporary fix to dockerfile (#150) @jdkent\n* [MAINT] require python3 (#147) @jdkent\n* [ENH] add visualizations (#148) @jdkent\n* [ENH] Add Docker and Singularity Support (#140) @PeerHerholz\n* [DOC] edit docs (#142) @jdkent\n* [DOC] Tiny tweak to README (#141) @njvack\n* [WIP] JOSS Paper (#122) @jdkent\n\n0.2.3 (January 29, 2019)\n------------------------\n\nVarious documentation and testing changes.\nWe will be using readthedocs going forward and not doctr.\n\n* [FIX] Remove high_pass references from documentation (#90) @RaginSagan\n* [FIX] Update betaseries.rst (#91) @ilkayisik\n* [ENH] autogenerate test data (#93) @jdkent\n* [FIX] add codecov back into testing (#94) @jdkent\n* [FIX] refactor dependencies (#95) @jdkent\n* [ENH] add example (#99) @jdkent\n* [FIX] first pass at configuring doctr (#100) @jdkent\n* [FIX] configure doctr (#101) @jdkent\n* [FIX] track version with docs (#102) @jdkent\n* [ENH] add sphinx versioning (#104) @jdkent\n* [FIX] first pass at simplifying example (#106) @jdkent\n* [FIX] add master back in to docs (#107) @jdkent\n* [MAINT] use readthedocs (#109) @jdkent\n* [DOC] add explicit download instruction (#112) @jdkent\n* [FIX] add graphviz as dependency for building docs (#115) @jdkent\n* [FIX] remove redundant/irrelevant doc building options (#116) @jdkent\n* [DOC] fix links in docs (#114) @PeerHerholz\n* [FIX,MAINT] rm 3.4 and test add 3.7 (#121) @jdkent\n* [FIX] pybids link (#120) @PeerHerholz\n* [FIX] syntax links (#119) @PeerHerholz\n\n0.2.2 (November 15, 2018)\n-------------------------\n\nQuick 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