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Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.13.1

Gorgolewski, Krzysztof J.; Esteban, Oscar; Ellis, David Gage; Notter, Michael Philipp; Ziegler, Erik; Johnson, Hans; Hamalainen, Carlo; Yvernault, Benjamin; Burns, Christopher; Manhães-Savio, Alexandre; Jarecka, Dorota; Markiewicz, Christopher J.; Salo, Taylor; Clark, Daniel; Waskom, Michael; Wong, Jason; Modat, Marc; Dewey, Blake E; Clark, Michael G.; Dayan, Michael; Loney, Fred; Madison, Cindee; Gramfort, Alexandre; Keshavan, Anisha; Berleant, Shoshana; Pinsard, Basile; Goncalves, Mathias; Clark, Dav; Cipollini, Ben; Varoquaux, Gael; Wassermann , Demian; Rokem, Ariel; Halchenko, Yaroslav O.; Forbes, Jessica; Moloney, Brendan; Malone, Ian B.; Hanke, Michael; Mordom, David; Buchanan, Colin; Pauli, Wolfgang M.; Huntenburg, Julia M.; Horea, Christian; Schwartz, Yannick; Tungaraza, Rosalia; Iqbal, Shariq; Kleesiek, Jens; Sikka, Sharad; Frohlich, Caroline; Kent, James; Perez-Guevara, Martin; Watanabe, Aimi; Welch, David; Cumba, Chad; Ginsburg, Daniel; Eshaghi, Arman; Kastman, Erik; Bougacha, Salma; Blair, Ross; Acland, Benjamin; Gillman, Ashley; Schaefer, Alexander; Nichols, B. Nolan; Giavasis, Steven; Erickson, Drew; Correa, Carlos; Ghayoor, Ali; Küttner, René; Haselgrove, Christian; Zhou, Dale; Craddock, R. Cameron; Haehn, Daniel; Lampe, Leonie; Millman, Jarrod; Lai, Jeff; Renfro, Mandy; Liu, Siqi; Stadler, Jörg; Glatard, Tristan; Kahn, Ari E.; Kong, Xiang-Zhen; Triplett, William; Park, Anne; McDermottroe, Conor; Hallquist, Michael; Poldrack, Russell; Perkins, L. Nathan; Noel, Maxime; Gerhard, Stephan; Salvatore, John; Mertz, Fred; Broderick, William; Inati, Souheil; Hinds, Oliver; Brett, Matthew; Durnez, Joke; Tambini, Arielle; Rothmei, Simon; Andberg, Sami Kristian; Cooper, Gavin; Marina, Ana; Mattfeld, Aaron; Urchs, Sebastian; Sharp, Paul; Matsubara, K; Geisler, Daniel; Cheung, Brian; Floren, Andrew; Nickson, Thomas; Pannetier, Nicolas; Weinstein, Alejandro; Dubois, Mathieu; Arias, Jaime; Tarbert, Claire; Schlamp, Kai; Jordan, Kesshi; Liem, Franz; Saase, Victor; Harms, Robbert; Khanuja, Ranjeet; Podranski, Kornelius; Flandin, Guillaume; Papadopoulos Orfanos, Dimitri; Schwabacher, Isaac; McNamee, Daniel; Falkiewicz, Marcel; Pellman, John; Linkersdörfer, Janosch; Varada, Jan; Pérez-García, Fernando; Davison, Andrew; Shachnev, Dmitry; Ghosh, Satrajit

0.13.1 (May 20, 2017)

  • FIX: Make release compatible with conda-forge build process (https://github.com/nipy/nipype/pull/2017)
  • ENH: Update some minimum versions in compliance with Debian Jessie (https://github.com/nipy/nipype/pull/2017)
  • ENH: Circle builds use cached docker layers (https://github.com/nipy/nipype/pull/2017)
  • ENH: Base docker to use FS6 and ANTS 2.2.0 (https://github.com/nipy/nipype/pull/2024)
  • FIX: Mailmap and contributor acknowledgment (https://github.com/nipy/nipype/pull/2017)
  • FIX: Preserve node properties in sub nodes of MapNode (https://github.com/nipy/nipype/pull/2019)
  • FIX: Fix interfaces 3DUnifize, ICA_AROMA, BinaryMaths, RegAverage, BBRegister, AffineInitializer (https://github.com/nipy/nipype/pull/2025, https://github.com/nipy/nipype/pull/2027, https://github.com/nipy/nipype/pull/2036, https://github.com/nipy/nipype/pull/2037, https://github.com/nipy/nipype/pull/2031, https://github.com/nipy/nipype/pull/2010)
  • ENH: Add Anisotropic Power interface (https://github.com/nipy/nipype/pull/2039)
  • FIX: Bayesian estimation in SPM (https://github.com/nipy/nipype/pull/2030)

0.13.0 (May 11, 2017)

  • ENH: Multi-stage recon-all directives (https://github.com/nipy/nipype/pull/1991)
  • FIX: FEAT "folder does not exist" error (https://github.com/nipy/nipype/pull/2000)
  • ENH: Niftyfit interfaces (https://github.com/nipy/nipype/pull/1910)
  • FIX: Define ANTSPATH for BrainExtraction automatically (https://github.com/nipy/nipype/pull/1986)
  • ENH: New trait for imaging files (https://github.com/nipy/nipype/pull/1949)
  • ENH: Niftyseg interfaces (https://github.com/nipy/nipype/pull/1911)
  • ENH: Niftyreg interfaces (https://github.com/nipy/nipype/pull/1913)
  • MRG: Allow more support for CLI (https://github.com/nipy/nipype/pull/1908)
  • ENH: 3dQwarpPlusMinus interface (https://github.com/nipy/nipype/pull/1974)
  • FIX: PY3.6 support (https://github.com/nipy/nipype/pull/1977)
  • FIX: PY3 and stream fixes for MRTrix2TrackVis (https://github.com/nipy/nipype/pull/1804)
  • ENH: More mask options for CompCor interfaces (https://github.com/nipy/nipype/pull/1968 + https://github.com/nipy/nipype/pull/1992)
  • ENH: Additional TOPUP outputs (https://github.com/nipy/nipype/pull/1976)
  • ENH: Additional Eddy flags (https://github.com/nipy/nipype/pull/1967)
  • ENH: ReconAll handlers for less common cases (https://github.com/nipy/nipype/pull/1966)
  • ENH: FreeSurferSource now finds graymid/midthickness surfs (https://github.com/nipy/nipype/pull/1972)
  • ENH: Additional fslmaths dimensional reduction operations (https://github.com/nipy/nipype/pull/1956)
  • ENH: More options for RobustFOV interface (https://github.com/nipy/nipype/pull/1923)
  • ENH: Add MRIsCombine to FreeSurfer utils (https://github.com/nipy/nipype/pull/1948)
  • FIX: Level1Design EV parameter substitution (https://github.com/nipy/nipype/pull/1953)
  • FIX: Dcm2niix outputs can be uncompressed (https://github.com/nipy/nipype/pull/1951)
  • FIX: Ensure build fails in Circle when tests fail (https://github.com/nipy/nipype/pull/1981)
  • ENH: Add interface to antsAffineInitializer (https://github.com/nipy/nipype/pull/1980)
  • ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840)
  • ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845)
  • FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (https://github.com/nipy/nipype/pull/1728)
  • FIX: Select Eddy run command at runtime (https://github.com/nipy/nipype/pull/1871)
  • FIX: Increase FLIRT's flexibility with apply_xfm (https://github.com/nipy/nipype/pull/1875)
  • DOC: Update FSL preprocess docstrings (https://github.com/nipy/nipype/pull/1881)
  • ENH: Support GIFTI outputs in SampleToSurface (https://github.com/nipy/nipype/pull/1886)
  • FIX: Configparser differences between PY2 and PY3 (https://github.com/nipy/nipype/pull/1890)
  • ENH: Add mris_expand interface (https://github.com/nipy/nipype/pull/1893)
  • FIX: Split over-eager globs in FreeSurferSource (https://github.com/nipy/nipype/pull/1894)
  • FIX: Store undefined by default so that xor checks don't trip (https://github.com/nipy/nipype/pull/1903)
  • FIX: Gantt chart generator PY3 compatibility (https://github.com/nipy/nipype/pull/1907)
  • FIX: Add DOF and --fsl-dof options to BBRegister (https://github.com/nipy/nipype/pull/1917)
  • ENH: Auto-derive input_names in Function (https://github.com/nipy/nipype/pull/1918)
  • FIX: Minor fixes for NonSteadyStateDetector (https://github.com/nipy/nipype/pull/1926)
  • DOC: Add duecredit references for AFNI and FSL (https://github.com/nipy/nipype/pull/1930)
  • ENH: Added zenodo (https://zenodo.org/) file (https://github.com/nipy/nipype/pull/1924)
  • ENH: Disable symlinks on CIFS filesystems (https://github.com/nipy/nipype/pull/1941)
  • ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896)
  • ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
  • ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
  • REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
  • FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813)
  • FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831)
  • ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827)
  • FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827)
  • ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828)
  • FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833)
  • FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825)
  • ENH: Revised all Dockerfiles and automated deployment to Docker Hub from CircleCI (https://github.com/nipy/nipype/pull/1815)
  • ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
  • FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777)
  • FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799)
  • ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793)
  • TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769)

0.13.0-rc1 (January 4, 2017)

  • FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770)
  • FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756)
  • TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751)
  • FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689)
  • REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
  • ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
  • FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
  • FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)
  • ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
  • ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627)
  • FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
  • TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
  • ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647)
  • ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
  • ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
  • ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599)
  • ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466)
  • FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572)
  • REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597)
  • REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593)
  • TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609)
  • ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554)
  • ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
  • ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
  • FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)
  • TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
  • ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
  • FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586)
  • ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
  • ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant (https://github.com/nipy/nipype/pull/1654)

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