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Published May 12, 2017 | Version 0.13.0
Software Open

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

Authors/Creators

  • 1. Department of Psychology, Stanford University
  • 2. Independent
  • 3. The University of Iowa
  • 4. UC Berkeley
  • 5. Shattuck Lab, UCLA Brain Mapping Center
  • 6. Mayo Clinic, Neurology, Rochester, MN, USA
  • 7. Klinikum rechts der Isar, TUM. ACPySS
  • 8. The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland
  • 9. University of Iowa
  • 10. Department of Electrical and Computer Engineering, Johns Hopkins University
  • 11. Dartmouth College: Hanover, NH, United States
  • 12. UC Berkeley - UCSF Graduate Program in Bioengineering
  • 13. Developer
  • 14. Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
  • 15. Otto-von-Guericke-University Magdeburg, Germany
  • 16. SRI International
  • 17. Athena EPI, Inria Sophia-Antipolis
  • 18. University College London
  • 19. Boston University
  • 20. INRIA
  • 21. Washington University in St Louis
  • 22. The University of Washington eScience Institute
  • 23. State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
  • 24. CNRS LTCI, Telecom ParisTech, Université Paris-Saclay
  • 25. UniversityHospital Heidelberg, Germany
  • 26. National University Singapore
  • 27. Nathan s Kline institute for psychiatric research
  • 28. Neurospin/Unicog/Inserm/CEA
  • 29. 1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montréal, 3801 University Street, WB-208, H3A 2B4, Québec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.
  • 30. Duke University
  • 31. The University of Sydney
  • 32. University of illinois urbana champaign
  • 33. Mayo Clinic
  • 34. Harvard University - Psychology
  • 35. MPI CBS Leipzig, Germany
  • 36. Child Mind Institite
  • 37. Technische Universität Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry
  • 38. Institute of Neuroinformatics, ETH/University of Zurich
  • 39. Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
  • 40. German Institute for International Educational Research
  • 41. Max Planck Research Group for Neuroanatomy & Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
  • 42. University of Helsinki
  • 43. Leibniz Institute for Neurobiology
  • 44. MPI-CBS; McGill University
  • 45. UC San Diego
  • 46. University of Newcastle, Australia
  • 47. The University of Texas at Austin
  • 48. State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
  • 49. Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
  • 50. University of Cambridge
  • 51. CEA
  • 52. Child Mind Institute / Nathan Kline Institute
  • 53. MIT
  • 54. Department of Psychology, Stanford University; Parietal, INRIA
  • 55. MIT, HMS

Description

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)

Files

nipy/nipype-0.13.0.zip

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Additional details

Related works

Is new version of
10.5281/zenodo.50186 (DOI)
Is supplemented by
https://github.com/nipy/nipype/releases/tag/0.13.0 (URL)