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Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.12.0-rc1

Name: Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.13.0
Keywords: neuroimaging, workflow, pipeline

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 21 Apr 2016Publisher:Zenodo

Authors: Gorgolewski, Krzysztof J.; Esteban, Oscar; Ellis, David Gage; Notter, Michael Philipp; Ziegler, Erik; Johnson, Hans; Hamalainen, Carlo; +125 Authors

doi: 10.5281/zenodo.575897 , 10.5281/zenodo.581704 , 10.5281/zenodo.50186

Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.12.0-rc1

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Abstract

Release 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) 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)

Related Organizations

The University of Texas at Austin
United States
National University of Singapore
Singapore
Johns Hopkins University
United States
State Key Laboratory of Cognitive Neuroscience and Learning
China (People's Republic of)
Boston University
United States

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Keywords

neuroimaging, workflow, pipeline

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