1.0.2

1.0.2 (March 27, 2018)

Full changelog

• FIX: dcm2niix interface (#2498)
• FIX: mark .niml.dset as special extension in utils.filemanip (#2495)
• FIX: handle automatic module creation, name extraction, default value (#2490)
• FIX: Check and report mount table parsing failures (#2476)
• FIX: Check against full node name when reconnecting JoinNodes (#2479)
• DOC: Add tutorials, porcupine to users TOC (#2503)
• DOC: Contributing and testing (#2482)
• DOC: Describe 'orphaned' tag in CONTRIBUTING (#2481)
• DOC: Add details for dcm2niix output filename pattern (#2512)
• ENH: Add interface for AFNI 3dNwarpAdjust (#2450)
• ENH: Update SSHDataGrabber to fetch related files (#2104)
• ENH: Add interpolation order parameter to NiftyReg's RegTools (#2471)
• MAINT: Stray warnings and exceptions (#2478)
• MAINT: Add dev install option, update CONTRIBUTING (#2477)
• MAINT: Sync requirements with info.py (#2472)
• CI: Update Travis builds, Docker to use latest miniconda (#2455)
• TEST: Parallelize pytest (#2469)

1.0.1

1.0.1 (February 27, 2018)

Full changelog

• FIX: Small bug in freesurfer label2annot fill_thresh specs #2377
• FIX: Error creating gradients in DTIRecon #2460
• FIX: improve matlab_cmd #2452
• FIX: Extract unit information from image header in CompCor #2458
• FIX: Update pybids data directory, unbundle out-of-date numpydoc #2437
• FIX: Out_file bugs in Afni.Zcat and Afni.Merge interfaces #2424
• FIX: Re-enable spm.Realign to take lists of lists of files #2409
• FIX: Remove deprecated output from ICC interface #2422
• FIX: Argstr for mask in Afni.BlurToFWHM #2418
• FIX: Default value for sbatch_args (SLURMGraph) #2417
• FIX: Ortvec argstr for Afni.Deconvolve #2415
• FIX: Bug fixes for afni.model #2398
• DOC: Add brief neurodocker tutorial #2464
• DOC: Fix tutorials #2459
• ENH: antsRegistrationSyNQuick interface #2453
• ENH: Automate updates of CHANGES #2440
• ENH: Add SPM Fieldmap Tool wrapper #1905
• ENH: Additional option for DataGrabber #1915
• ENH: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve #2426
• ENH: c3d/c4d interface #2430
• ENH: Allow input weight for AFNI's volreg. #2396
• ENH: Delay crashing if exception is raised in local hash check #2410
• CI: Add doctests to pytest script #2449
• CI: Ignore tests in calculating coverage #2443
• CI: Saturate Circle workflow #2386
• REF: Update and factor mount table parsing #2444
• REF: Make ignore_exception a class attribute #2414

Nipype - v1.0.0

1.0.0 (January 25, 2018)

Full changelog

• FIX: PBS plugin submissions (#2344)
• FIX: Graph plugins submissions (#2359)
• FIX: Logging error if % in interface command (#2364)
• FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (#2373)
• FIX: Cluster threshold in randomise + change default prefix (#2369)
• FIX: Errors parsing $DISPLAY (#2363)
• FIX: MultiProc starting workers at dubious wd (#2368)
• FIX: Explicitly collect MultiProc job IDs (#2378)
• FIX: Correct Windows environment canonicalization (#2328)
• FIX: Linked libraries (#2322)
• REF+FIX: Move BIDSDataGrabber to interfaces.io + fix correct default behavior (#2336)
• REF+MAINT: Simplify hashing (#2383)
• MAINT: Cleanup Interfaces base (#2387)
• MAINT: Cleanup EngineBase (#2376)
• MAINT: Cleaning / simplify Node (#2325)
• MAINT+ENH: Update and extend MRtrix3 interfaces (#2338)
• ENH: Add AFNI interface for 3dConvertDset (#2337)
• ENH: Allow specific interface command prefixes (#2379)
• STY: Cleanup of PEP8 violations (#2358)
• STY: Cleanup of trailing spaces and adding of missing newlines at end of files (#2355)
• STY: Apply yapf to codebase (#2371)
• DOC: Updated guide for contributing (#2393)

0.14.0

0.14.0 (November 29, 2017)

Full changelog

• FIX+MAINT: Revision of the resource monitor (#2285)
• FIX: MultiProc mishandling crashes (#2301)
• MAINT: Revise use of subprocess.Popen (#2289)
• ENH: Memorize version checks (#2274, #2295)

0.14.0-rc1

0.14.0rc1 (November 21, 2017)

• ENH: Generate Dockerfiles with neurodocker (#2202)
• ENH: FLAIR options for recon-all (#2279)
• ENH: Config option for setting maxtasksperchild when multiprocessing (#2284)
• FIX: Testing maintainance and improvements (#2252)
• ENH: Add elapsed_time and final metric_value to ants.Registration (#1985)
• ENH: Improve terminal_output feature (#2209)
• ENH: Simple interface to FSL std2imgcoords (#2209, prev #1398)
• ENH: Centralize virtual/physical $DISPLAYs (#2203, #2211)
• ENH: New ResourceMonitor - replaces resource profiler (#2200)
• ENH: Quickshear interface (#2047)
• MAINT: updated deprecated HasTraits method (#2048)
• ENH: CLI versioning (#2054)
• ENH: Dual Regression interface (#2057)
• ENH: Additional args to ANTs registration (#2062, #2078)
• FIX: Mp2rage interfaces updated for new parameter names in cbstools 3 (#2065)
• MAINT: Removed automatic nipype folder creation in HOME (#2076)
• MAINT: Additional Windows support (#2085)
• ENH: Output realignment matrices from TOPUP (#2084)
• ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize,
  3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (#2087, #2090,
  #2095, #2099, #2103,
  #2114, #2135, #2186,
  #2201, #2210)
• MAINT: cleanup and update AFNI's Allineate (#2098)
• ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (#2107, https://github.com/nipy/nipype/pull/#2122)
• FIX: Catch more dcm2niix DTI conversions (#2110)
• FIX: Retrieve aseg + wmparc stats properly (#2117)
• ENH: ANTs MeasureImageSimilarity Inteface (#2128)
• FIX: CompCor filter_basis of correct size, pre-filter column headers (#2136, #2138)
• ENH: FreeSurfer lta_convert and mri_coreg interfaces (#2140, #2172)
• ENH: Speed up S3DataGrabber (#2143)
• FIX: Allow S3DataGrabber to grab single file (#2147)
• FIX: Allow 4D images as inputs to buildtemplateparallel.sh and N4BiasFieldCorrection (#2151)
• MAINT: Detect and warn unconnected duplicate nodes (#2163)
• ENH: Calcmedian Interface (#2167)
• FIX: probtrackx2 outputs (#2169)
• ENH: Improve FreeSurfer registration (#2172)
• ENH: BIDSDataGrabber interface (#2174)
• MAINT: Set minimum numpy version to 1.9.0 (#2182)
• ENH: Support for multiple intial-moving-transforms (#2187)
• MAINT: Fixes for networkx and afni (#2196, #2171)
• TST: Update C3D version in Docker build (#2199)
• ENH: SimpleInterface interface (#2220)
• ENH: Add LTA to Tkregister2 (#2217)

Release 0.13.1

0.13.1 (May 20, 2017)

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

0.13.0 (May 11, 2017)

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

0.13.0-rc1 (January 4, 2017)

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

Release 0.13.0

Release 0.13.0 (May 11, 2017)

• ENH: Multi-stage recon-all directives (#1991)
• FIX: FEAT "folder does not exist" error (#2000)
• ENH: Niftyfit interfaces (#1910)
• FIX: Define ANTSPATH for BrainExtraction automatically (#1986)
• ENH: New trait for imaging files (#1949)
• ENH: Niftyseg interfaces (#1911)
• ENH: Niftyreg interfaces (#1913)
• MRG: Allow more support for CLI (#1908)
• ENH: 3dQwarpPlusMinus interface (#1974)
• FIX: PY3.6 support (#1977)
• FIX: PY3 and stream fixes for MRTrix2TrackVis (#1804)
• ENH: More mask options for CompCor interfaces (#1968 + #1992)
• ENH: Additional TOPUP outputs (#1976)
• ENH: Additional Eddy flags (#1967)
• ENH: ReconAll handlers for less common cases (#1966)
• ENH: FreeSurferSource now finds graymid/midthickness surfs (#1972)
• ENH: Additional fslmaths dimensional reduction operations (#1956)
• ENH: More options for RobustFOV interface (#1923)
• ENH: Add MRIsCombine to FreeSurfer utils (#1948)
• FIX: Level1Design EV parameter substitution (#1953)
• FIX: Dcm2niix outputs can be uncompressed (#1951)
• FIX: Ensure build fails in Circle when tests fail (#1981)
• ENH: Add interface to antsAffineInitializer (#1980)
• ENH: AFNI motion parameter support for FrameWiseDisplacement (#1840)
• ENH: Add ANTs KellyKapowski interface (#1845)
• FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (#1728)
• FIX: Select Eddy run command at runtime (#1871)
• FIX: Increase FLIRT's flexibility with apply_xfm (#1875)
• DOC: Update FSL preprocess docstrings (#1881)
• ENH: Support GIFTI outputs in SampleToSurface (#1886)
• FIX: Configparser differences between PY2 and PY3 (#1890)
• ENH: Add mris_expand interface (#1893)
• FIX: Split over-eager globs in FreeSurferSource (#1894)
• FIX: Store undefined by default so that xor checks don't trip (#1903)
• FIX: Gantt chart generator PY3 compatibility (#1907)
• FIX: Add DOF and --fsl-dof options to BBRegister (#1917)
• ENH: Auto-derive input_names in Function (#1918)
• FIX: Minor fixes for NonSteadyStateDetector (#1926)
• DOC: Add duecredit references for AFNI and FSL (#1930)
• ENH: Added zenodo (https://zenodo.org/) file (#1924)
• ENH: Disable symlinks on CIFS filesystems (#1941)
• ENH: Sphinx extension to plot workflows (#1896)
• ENH: Added non-steady state detector for EPI data (#1839)
• ENH: Enable new BBRegister init options for FSv6+ (#1811)
• REF: Splits nipype.interfaces.utility into base, csv, and wrappers (#1828)
• FIX: Makespec now runs with nipype in current directory (#1813)
• FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (#1796 + #1831)
• ENH: DVARS includes intensity normalization feature - turned on by default (#1827)
• FIX: DVARS is correctly using sum of squares instead of standard deviation (#1827)
• ENH: Refactoring of nipype.interfaces.utility (#1828)
• FIX: CircleCI were failing silently. Some fixes to tests (#1833)
• FIX: Issues in Docker image permissions, and docker documentation (#1825)
• ENH: Revised all Dockerfiles and automated deployment to Docker Hub
  from CircleCI (#1815)
• ENH: Update ReconAll interface for FreeSurfer v6.0.0 (#1790)
• FIX: Cast DVARS float outputs to avoid memmap error (#1777)
• FIX: FSL FNIRT intensity mapping files (#1799)
• ENH: Additional outputs generated by FSL EDDY (#1793)
• TST: Parallelize CircleCI build across 4 containers (#1769)
• FIX: Compatibility with traits 4.6 (#1770)
• FIX: Multiproc deadlock (#1756)
• TST: Replace nose and unittest with pytest (#1722, #1751)
• FIX: Semaphore capture using MultiProc plugin (#1689)
• REF: Refactor AFNI interfaces (#1678, #1680)
• ENH: Move nipype commands to group command using click (#1608)
• FIX: AFNI Retroicor interface fixes (#1669)
• FIX: Minor errors after migration to setuptools (#1671)
• ENH: Add AFNI 3dNote interface (#1637)
• ENH: Abandon distutils, only use setuptools (#1627)
• FIX: Minor bugfixes related to unicode literals (#1656)
• TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
• ENH: Add signal extraction interface (#1647)
• ENH: Add a DVARS calculation interface (#1606)
• ENH: New interface to b0calc of FSL-POSSUM (#1399)
• ENH: Add CompCor (#1599)
• ENH: Add duecredit entries (#1466)
• FIX: Python 3 compatibility fixes (#1572)
• REF: Improved PEP8 compliance for fsl interfaces (#1597)
• REF: Improved PEP8 compliance for spm interfaces (#1593)
• TST: Replaced coveralls with codecov (#1609)
• ENH: More BrainSuite interfaces (#1554)
• ENH: Convenient load/save of interface inputs (#1591)
• ENH: Add a Framewise Displacement calculation interface (#1604)
• FIX: Use builtins open and unicode literals for py3 compatibility (#1572)
• TST: reduce the size of docker images & use tags for images (#1564)
• ENH: Implement missing inputs/outputs in FSL AvScale (#1563)
• FIX: Fix symlink test in copyfile (#1570, #1586)
• ENH: Added support for custom job submission check in SLURM (#1582)
• ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
  (#1654)

0.13.0 Release candidate 1

Merge pull request #1772 from satra/rel/0.13.0-rc1

Rel/0.13.0 rc1

Patch to disable psutils by default

Release 0.12.1 (August 3, 2016)

• FIX: runtime profiling is optional and off by default (#1561)
• TST: circle CI tests run with docker (#1541)
• FIX: workflow export functions without import error (#1552)

0.12.0

Release 0.12.0 (July 12, 2016)

• ENH: New interface for Bruker to Nifti converter (#1523)
• FIX: output file naming for FIRST outputs (#1524)
• ENH: Adds fslmaths -Tstd to maths interfaces (#1518)
• FIX: Selecting "gamma" in FSL Level1Design now does what the name says (#1500)
• ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(#1493)
• ENH: ResourceMultiProc plugin to support resource allocation (#1372)
• ENH: Added dcm2niix interface (#1435)
• ENH: Add nipype_crash_search command (#1422)
• ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (#1305)
• FIX: job execution on systems/approaches where locale is undefined (#1401)
• FIX: Clean up byte/unicode issues using subprocess (#1394)
• FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (#973)
• ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
  (#1090)
• ENH: Added interfaces of AFNI (#1360,
  #1361, #1382)
• ENH: Provides a Nipype wrapper for antsJointFusion (#1351)
• ENH: Added support for PETPVC (#1335)
• ENH: Merge S3DataSink into DataSink, added AWS documentation (#1316)
• TST: Cache APT in CircleCI (#1333)
• ENH: Add new flags to the BRAINSABC for new features (#1322)
• ENH: Provides a Nipype wrapper for ANTs DenoiseImage (#1291)
• FIX: Minor bugfix logging hash differences (#1298)
• FIX: Use released Prov python library (#1279)
• ENH: Support for Python 3 (#1221)
• FIX: VTK version check missing when using tvtk (#1219)
• ENH: Added an OAR scheduler plugin (#1259)
• ENH: New ANTs interface: antsBrainExtraction (#1231)
• API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
• ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (#1201)
• ENH: Interfaces for MINC tools (#1304)
• FIX: Use realpath to determine hard link source (#1388)
• FIX: Correct linking/copying fallback behavior (#1391)
• ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (#1326)
• FIX: Permit relative path for concatenated_file input to Concatenate() (#1411)
• ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (#1434)
• ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
  (#1460)