Home · Quickstart · User Guide and Examples · Interfaces Index · Developers · About · Nipy

# 0.14.0 (November 29, 2017)

(Full changelog)

- FIX+MAINT: Revision of the resource monitor (https://github.com/nipy/nipype/pull/2285)

- FIX: MultiProc mishandling crashes (https://github.com/nipy/nipype/pull/2301)

- MAINT: Revise use of subprocess.Popen (https://github.com/nipy/nipype/pull/2289)

- ENH: Memorize version checks (https://github.com/nipy/nipype/pull/2274, https://github.com/nipy/nipype/pull/2295)

## 0.14.0rc1 (November 21, 2017)

- ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)

- ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)

- ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)

- FIX: Testing maintenance and improvements (https://github.com/nipy/nipype/pull/2252)

- ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)

- ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)

- ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)

- ENH: Centralize virtual/physical $DISPLAYs (https://github.com/nipy/nipype/pull/2203, https://github.com/nipy/nipype/pull/2211)

- ENH: New ResourceMonitor - replaces resource profiler (https://github.com/nipy/nipype/pull/2200)

- ENH: Quickshear interface (https://github.com/nipy/nipype/pull/2047)

- MAINT: updated deprecated HasTraits method (https://github.com/nipy/nipype/pull/2048)

- ENH: CLI versioning (https://github.com/nipy/nipype/pull/2054)

- ENH: Dual Regression interface (https://github.com/nipy/nipype/pull/2057)

- ENH: Additional args to ANTs registration (https://github.com/nipy/nipype/pull/2062, https://github.com/nipy/nipype/pull/2078)

- FIX: Mp2rage interfaces updated for new parameter names in cbstools 3 (https://github.com/nipy/nipype/pull/2065)

- MAINT: Removed automatic nipype folder creation in HOME (https://github.com/nipy/nipype/pull/2076)

- MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085)

- ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084)

- ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize,

    3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103, https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186, https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210)

- MAINT: cleanup and update AFNI’s Allineate (https://github.com/nipy/nipype/pull/2098)

- ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)

- FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)

- FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)

- ENH: ANTs MeasureImageSimilarity Interface (https://github.com/nipy/nipype/pull/2128)

- FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)

- ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)

- ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)

- FIX: Allow S3DataGrabber to grab single file (https://github.com/nipy/nipype/pull/2147)

- FIX: Allow 4D images as inputs to buildtemplateparallel.sh and N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/2151)

- MAINT: Detect and warn unconnected duplicate nodes (https://github.com/nipy/nipype/pull/2163)

- ENH: Calcmedian Interface (https://github.com/nipy/nipype/pull/2167)

- FIX: probtrackx2 outputs (https://github.com/nipy/nipype/pull/2169)

- ENH: Improve FreeSurfer registration (https://github.com/nipy/nipype/pull/2172)

- ENH: BIDSDataGrabber interface (https://github.com/nipy/nipype/pull/2174)

- MAINT: Set minimum numpy version to 1.9.0 (https://github.com/nipy/nipype/pull/2182)

- ENH: Support for multiple intial-moving-transforms (https://github.com/nipy/nipype/pull/2187)

- MAINT: Fixes for networkx and afni (https://github.com/nipy/nipype/pull/2196, https://github.com/nipy/nipype/pull/2171)

- TST: Update C3D version in Docker build (https://github.com/nipy/nipype/pull/2199)

- ENH: SimpleInterface interface (https://github.com/nipy/nipype/pull/2220)

- ENH: Add LTA to Tkregister2 (https://github.com/nipy/nipype/pull/2217)

# 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)

# Release 0.12.1 (August 3, 2016)

- FIX: runtime profiling is optional and off by default (https://github.com/nipy/nipype/pull/1561)

- TST: circle CI tests run with docker (https://github.com/nipy/nipype/pull/1541)

- FIX: workflow export functions without import error (https://github.com/nipy/nipype/pull/1552)

# Release 0.12.0 (July 12, 2016)

- ENH: New interface for Bruker to Nifti converter (https://github.com/nipy/nipype/pull/1523)

- FIX: output file naming for FIRST outputs (https://github.com/nipy/nipype/pull/1524)

- ENH: Adds fslmaths -Tstd to maths interfaces (https://github.com/nipy/nipype/pull/1518)

- FIX: Selecting “gamma” in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)

- ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)

- ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)

- ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)

- ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)

- ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)

- FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)

- FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)

- FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)

- ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography

    (https://github.com/nipy/nipype/pull/1090)

- ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,

    https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)

- ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)

- ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)

- ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)

- TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)

- ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)

- ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)

- FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)

- FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)

- ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)

- FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)

- ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)

- ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/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 (https://github.com/nipy/nipype/pull/1201)

- ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)

- FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)

- FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)

- ENH: Nipype workflow and interfaces for FreeSurfer’s recon-all (https://github.com/nipy/nipype/pull/1326)

- FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)

- ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)

- ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg

    (https://github.com/nipy/nipype/pull/1460)

# Release 0.11.0 (September 15, 2015)

- API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)

- ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets

    (https://github.com/nipy/nipype/pull/889).

- ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)

- ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)

- FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)

- BUG: ANTs Registration interface failed with multi-modal inputs

    (https://github.com/nipy/nipype/pull/1176) (https://github.com/nipy/nipype/issues/1175)

- ENH: dipy.TrackDensityMap interface now accepts a reference image (https://github.com/nipy/nipype/pull/1091)

- FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)

- ENH: Attempt to use hard links for data sink.

    (https://github.com/nipy/nipype/pull/1161)

- FIX: Updates to SGE Plugins

    (https://github.com/nipy/nipype/pull/1129)

- ENH: Add ants JointFusion() node with testing

    (https://github.com/nipy/nipype/pull/1160)

- ENH: Add –float option for antsRegistration calls

    (https://github.com/nipy/nipype/pull/1159)

- ENH: Added interface to simulate DWIs using the multi-tensor model

    (https://github.com/nipy/nipype/pull/1085)

- ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)

- ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (https://github.com/nipy/nipype/pull/1136)

- FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,

    replaced by https://github.com/nipy/nipype/pull/1093)

- ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings

    (https://github.com/nipy/nipype/pull/1016)

- FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,

    fix bug in area weighted distance, and added optimizations (https://github.com/nipy/nipype/pull/1016)

- ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)

- FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)

- ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.

    (https://github.com/nipy/nipype/pull/1019)

- FIX: In the FSLXcommand _list_outputs function fixed for loop range (https://github.com/nipy/nipype/pull/1071)

- ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)

- FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)

- ENH: Added “nipype_cmd” tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)

- FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)

- ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)

- ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)

- ENH: Improve JSON interfaces: default settings when reading and consistent output creation

    when writing (https://github.com/nipy/nipype/pull/1047)

- FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)

- FIX: Removed unused ANTS registration flag (https://github.com/nipy/nipype/pull/999)

- FIX: Amend create_tbss_non_fa() workflow to match FSL’s tbss_non_fa command. (https://github.com/nipy/nipype/pull/1033)

- FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)

- ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)

- FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)

- ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)

- ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)

- BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)

- FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)

- ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)

- ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.

    New options also include choice of tracker, interpolator, stepsize and curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)

- FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)

- FIX: Bug crashed ‘make api’ (https://github.com/nipy/nipype/pull/1026)

- ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)

- ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made

    argument formatting consistent. Cleaned ants.segmentation according to PEP8. (https://github.com/nipy/nipype/pull/990/files)

- ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)

- FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)

- FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)

- ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)

- FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is

    undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)

- FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)

- FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)

- ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)

- ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)

- ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)

- FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)

- FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)

- FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)

- FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)

- ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)

- FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)

- ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)

- ENH: Use a while loop to wait for Xvfb (up to a max wait time “xvfb_max_wait” in config file, default 10)

    (https://github.com/nipy/nipype/pull/1142)

# Release 0.10.0 (October 10, 2014)

- ENH: New miscellaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)

    to enable parallel processing of very large images.

- ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still

    available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU

- ENH: Added experimental support for MIPAV algorithms through JIST plugins

- ENH: New dipy interfaces: Denoise, Resample

- ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess

- ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp

- ENH: New miscellaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise

- ENH: New AFNI interfaces: Eval, Means, SVMTest, SVMTrain

- ENH: FUGUE interface has been refactored to use the name_template system, 3 examples

    added to doctests, some bugs solved.

- API: Interfaces to external packages are no longer available in the top-level

    `nipype` namespace, and must be imported directly (e.g. `from nipype.interfaces import fsl`).

- ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,

    AnalyzeWarp, PointsWarp, and EditTransform

- ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness

- ENH: New Diffusion Toolkit interface: TrackMerge

- ENH: New MRtrix interface: FilterTracks

- ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap

    are found in nipype.algorithms.metrics instead of misc. Overlap interface extended to allow files containing multiple ROIs and volume physical units.

- ENH: New interface in algorithms.metrics: ErrorMap (a voxel-wise diff map).

- ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()

- ENH: Deep revision of workflows for correction of dMRI artifacts. New dmri_preprocessing

    example.

- ENH: New data grabbing interface that works over SSH connections, SSHDataGrabber

- ENH: New color mode for write_graph

- ENH: You can now force MapNodes to be run serially

- ENH: Added ANTS based openfmri workflow

- ENH: MapNode now supports flattening of nested lists

- ENH: Support for headless mode using Xvfb

- ENH: nipype_display_crash has a debugging mode

- FIX: MRTrix tracking algorithms were ignoring mask parameters.

- FIX: FNIRT registration pathway and associated OpenFMRI example script

- FIX: spm12b compatibility for Model estimate

- FIX: Batch scheduler controls the number of maximum jobs properly

- FIX: Update for FSL 5.0.7 which deprecated Contrast Manager

# Release 0.9.2 (January 31, 2014)

- FIX: DataFinder was broken due to a typo

- FIX: Order of DataFinder outputs was not guaranteed, it’s human sorted now

- ENH: New interfaces: Vnifti2Image, VtoMat

# Release 0.9.1 (December 25, 2013)

- FIX: installation issues

# Release 0.9.0 (December 20, 2013)

- ENH: SelectFiles: a streamlined version of DataGrabber

- ENH: new tools for defining workflows: JoinNode, synchronize and itersource

- ENH: W3C PROV support with optional RDF export built into Nipype

- ENH: Added support for Simple Linux Utility Resource Management (SLURM)

- ENH: AFNI interfaces refactor, prefix, suffix are replaced by

    “flexible_%s_templates”

- ENH: New SPM interfaces:

    - spm.ResliceToReference,

    - spm.DicomImport

- ENH: New AFNI interfaces:

    - afni.AFNItoNIFTI

    - afni.TCorr1D

- ENH: Several new interfaces related to Camino were added:

    - camino.SFPICOCalibData

    - camino.Conmat

    - camino.QBallMX

    - camino.LinRecon

    - camino.SFPeaks

  One outdated interface no longer part of Camino was removed:

    - camino.Conmap

- ENH: Three new mrtrix interfaces were added:

    - mrtrix.GenerateDirections

    - mrtrix.FindShPeaks

    - mrtrix.Directions2Amplitude

- ENH: New FSL interfaces:

    - fsl.PrepareFieldmap

    - fsl.TOPUP

    - fsl.ApplyTOPUP

    - fsl.Eddy

- ENH: New misc interfaces:

    - FuzzyOverlap,

    - P2PDistance

- ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]

- ENH: Added simplified outputname generation for command line interfaces.

- ENH: Allow ants use a single mask image

- ENH: Create configuration option for parameterizing directories with hashes

- ENH: arrange nodes by topological sort with disconnected subgraphs

- ENH: uses the nidm iri namespace for uuids

- ENH: remove old reporting webpage

- ENH: Added support for Vagrant

- API: ‘name’ is now a positional argument for Workflow, Node, and MapNode constructors

- API: SPM now defaults to SPM8 or SPM12b job format

- API: DataGrabber and SelectFiles use human (or natural) sort now

- FIX: Several fixes related to Camino interfaces:

    - ProcStreamlines would ignore many arguments silently (target, waypoint, exclusion ROIS, etc.)

    - DTLUTGen would silently round the “step”, “snr” and “trace” parameters to integers

    - PicoPDFs would not accept more than one lookup table

    - PicoPDFs default pdf did not correspond to Camino default

    - Track input model names were outdated (and would generate an error)

    - Track numpds parameter could not be set for deterministic tractography

    - FA created output files with erroneous extension

- FIX: Deals properly with 3d files in SPM Realign

- FIX: SPM with MCR fixed

- FIX: Cleaned up input and output spec metadata

- FIX: example openfmri script now makes the contrast spec a hashed input

- FIX: FILMGLS compatibility with FSL 5.0.5

- FIX: Freesurfer recon-all resume now avoids setting inputs

- FIX: File removal from node respects file associations img/hdr/mat, BRIK/HEAD

# Release 0.8.0 (May 8, 2013)

- ENH: New interfaces: nipy.Trim, fsl.GLM, fsl.SigLoss, spm.VBMSegment, fsl.InvWarp,

    dipy.TensorMode

- ENH: Allow control over terminal output for commandline interfaces

- ENH: Added preliminary support for generating Python code from Workflows.

- ENH: New workflows for dMRI and fMRI pre-processing: added motion artifact correction

    with rotation of the B-matrix, and susceptibility correction for EPI imaging using fieldmaps. Updated eddy_correct pipeline to support both dMRI and fMRI, and new parameters.

- ENH: Minor improvements to FSL’s FUGUE and FLIRT interfaces

- ENH: Added optional dilation of parcels in cmtk.Parcellate

- ENH: Interpolation mode added to afni.Resample

- ENH: Function interface can accept a list of strings containing import statements

    that allow external functions to run without their imports defined in the function body

- ENH: Allow node configurations to override master configuration

- FIX: SpecifyModel works with 3D files correctly now.

# Release 0.7.0 (Dec 18, 2012)

- ENH: Add basic support for LSF plugin.

- ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant,

    afni.AutoTcorrelate, DcmStack

- ENH: New workflows: ants template building (both using ‘ANTS’ and the new ‘antsRegistration’)

- ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate),

    how to set SGE specific options (smri_ants_build_template_new)

- ENH: added no_flatten option to Merge

- ENH: added versioning option and checking to traits

- ENH: added deprecation metadata to traits

- ENH: Slicer interfaces were updated to version 4.1

# Release 0.6.0 (Jun 30, 2012)

- API: display variable no longer encoded as inputs in commandline interfaces

- ENH: input hash not modified when environment DISPLAY is changed

- ENH: support for 3d files for TSNR calculation

- ENH: Preliminary support for graph submission with SGE, PBS and Soma Workflow

- ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM, MRIsSmooth,

    NetworkBasedStatistic, Atropos, N4BiasFieldCorrection, ApplyTransforms, fs.MakeAverageSubject, epidewarp.fsl, WarpTimeSeriesImageMultiTransform, AVScale, mri_ms_LDA

- ENH: simple interfaces for spm

- FIX: CompCor component calculation was erroneous

- FIX: filename generation for AFNI and PRELUDE

- FIX: improved slicer module autogeneration

- FIX: added missing options for BBRegsiter

- FIX: functionality of remove_unnecessary_ouputs cleaned up

- FIX: local hash check works with appropriate inputs

- FIX: Captures all stdout from commandline programs

- FIX: Afni outputs should inherit from TraitedSpec

# Release 0.5.3 (Mar 23, 2012)

- FIX: SPM model generation when output units is in scans

# Release 0.5.2 (Mar 14, 2012)

- API: Node now allows specifying node level configuration for SGE/PBS clusters

- API: Logging to file is disabled by default

- API: New location of log file -> .nipype/nipype.cfg

- ENH: Changing logging options via config works for distributed processing

- FIX: Unittests on debian (logging and ipython)

# Release 0.5 (Mar 10, 2012)

- API: FSL defaults to Nifti when OUTPUTTYPE environment variable not found

- API: By default inputs are removed from Node working directory

- API: InterfaceResult class is now versioned and stores class type not instance

- API: Added FIRST interface

- API: Added max_jobs parameter to plugin_args. limits the number of jobs

    executing at any given point in time

- API: crashdump_dir is now a config execution option

- API: new config execution options for controlling hash checking, execution and

    logging behavior when running in distributed mode.

- API: Node/MapNode has new attribute that allows it to run on master thread.

- API: IPython plugin now invokes IPython 0.11 or greater

- API: Canned workflows are now all under a different package structure

- API: SpecifyModel event_info renamed to event_files

- API: DataGrabber is always being rerun (unless overwrite is set to False on

    Node level)

- API: “stop_on_first_rerun” does not stop for DataGrabber (unless overwrite is

    set to True on Node level)

- API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister,

    Normalize, Smooth)

- ENH: Added fsl resting state workflow based on behzadi 2007 CompCorr method.

- ENH: TSNR node produces mean and std-dev maps; allows polynomial detrending

- ENH: IdentityNodes are removed prior to execution

- ENH: Added Michael Notter’s beginner’s guide

- ENH: Added engine support for status callback functions

- ENH: SPM create warped node

- ENH: All underlying interfaces (including python ones) are now optional

- ENH: Added imperative programming option with Nodes and caching

- ENH: Added debug mode to configuration

- ENH: Results can be stored and loaded without traits exceptions

- ENH: Added concurrent log handler for distributed writing to log file

- ENH: Reporting can be turned off using config

- ENH: Added stats files to FreeSurferOutput

- ENH: Support for Condor through qsub emulation

- ENH: IdentityNode with iterable expansion takes place after remaining Identity

    Node removal

- ENH: Crashfile display script added

- ENH: Added FmriRealign4d node wrapped from nipy

- ENH: Added TBSS workflows and examples

- ENH: Support for openfmri data processing

- ENH: Package version check

- FIX: Fixed spm preproc workflow to cater to multiple functional runs

- FIX: Workflow outputs displays nodes with empty outputs

- FIX: SUSAN workflow works without usans

- FIX: SGE fixed for reading custom templates

- FIX: warping in SPM realign, Dartel and interpolation parameters

- FIX: Fixed voxel size parameter in freesurfer mri_convert

- FIX: 4D images in spm coregister

- FIX: Works around matlab tty bug

- FIX: Overwriting connection raises exception

- FIX: Outputs are loaded from results and not stored in memory for during

    distributed operation

- FIX: SPM threshold uses SPM.mat name and improved error detection

- FIX: Removing directory contents works even when a node has no outputs

- FIX: DARTEL workflows will run only when SPM 8 is available

- FIX: SPM Normalize estimate field fixed

- FIX: hashmethod argument now used for calculating hash of old file

- FIX: Modelgen now allows FSL style event files

# Release 0.4.1 (Jun 16, 2011)

- Minor bugfixes

# Release 0.4 (Jun 11, 2011)

- API: Timestamp hashing does not use ctime anymore. Please update your hashes by

    running workflows with updatehash=True option NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will rerun

- API: Workflow run function no longer supports (inseries, createdirsonly).

    Functions used in connect string must be pickleable

- API: SPM EstimateContrast: ignore_derivs replaced by use_derivs

- API: All interfaces: added new config option ignore_exception

- API: SpecifModel no longer supports (concatenate_runs, output_specs). high_pass_filter

    cutoff is mandatory (even if its set to np.inf). Additional interfaces SpecifySPMModel and SpecifySparseModel support other types of data.

- API: fsl.DTIFit input “save” is now called “save_tensor”

- API: All inputs of IdentityInterfaces are mandatory by default. You can turn

    this off by specifying mandatory_inputs=False to the constructor.

- API: fsl FILMGLS input “autocorr_estimate” is now called “autocorr_estimate_only”

- API: fsl ContrastMgr now requires access to specific files (no longer accepts

    the result directory)

- API: freesurfer.GLMFit input “surf” is now a boolean with three corresponding

    inputs – subject_id, hemi, and surf_geo

- ENH: All commandline interfaces display stdout and stderr

- ENH: All interfaces raise exceptions on error with an option to suppress

- ENH: Supports a plugin interface for execution (current support for multiprocessing,

    IPython, SGE, PBS)

- ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS

- ENH: Optionally allows keeping only required outputs

- ENH: New interface: utility.Rename to change the name of files, optionally

    using python string-formatting with inputs or regular expressions matching

- ENH: New interface: freesurfer.ApplyMask (mri_mask)

- ENH: New FSL interface – SwapDimensions (fslswapdim)

- ENH: Sparse models allow regressor scaling and temporal derivatives

- ENH: Added support for the component parts of FSL’s TBSS workflow (TBSSSkeleton

    and DistanceMap)

- ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images

- ENH: Added several higher-level interfaces to the fslmaths command:

    - ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths

- ENH: added support for networx 1.4 and improved iterable expansion

- ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines

- ENH: Ability to create a hierarchical dot file

- ENH: Improved debugging information for rerunning nodes

- ENH: Added ‘stop_on_first_rerun’ option

- ENH: Added support for Camino

- ENH: Added support for Camino2Trackvis

- ENH: Added support for Connectome Viewer

- BF: dcm2nii interface handles gzipped files correctly

- BF: FNIRT generates proper outputs

- BF: fsl.DTIFit now properly collects tensor volume

- BF: updatehash now removes old result hash file

# Release 0.3.4 (Jan 12, 2011)

- API: hash values for float use a string conversion up to the 10th decimal place.

- API: Iterables in output path will always be generated as _var1_val1_var2_val2 pairs

- ENH: Added support to nipy: GLM fit, contrast estimation and calculating mask from EPI

- ENH: Added support for manipulating surface files in Freesurfer:

    - projecting volume images onto the surface

    - smoothing along the surface

    - transforming a surface image from one subject to another

    - using tksurfer to save pictures of the surface

- ENH: Added support for flash processing using FreeSurfer

- ENH: Added support for flirt matrix in BBRegister

- ENH: Added support for FSL convert_xfm

- ENH: hashes can be updated again without rerunning all nodes.

- ENH: Added multiple regression design for FSL

- ENH: Added SPM based Analyze to Nifti converter

- ENH: Added increased support for PyXNAT

- ENH: Added support for MCR-based binary version of SPM

- ENH: Added SPM node for calculating various threshold statistics

- ENH: Added distance and dissimilarity measurements

- BF: Diffusion toolkit gets installed

- BF: Changed FNIRT interface to accept flexible lists (rather than 4-tuples)

    on all options specific to different subsampling levels

# Release 0.3.3 (Sep 16, 2010)

- API: subject_id in ModelSpec is now deprecated

- API: spm.Threshold - does not need mask, beta, RPV anymore - takes only one image (stat_image - mind the name change) - works with SPM2 SPM.mat - returns additional map - pre topological FDR

- ENH: Added support for Diffusion toolkit

- ENH: Added support for FSL slicer and overlay

- ENH: Added support for dcm2nii

- BF: DataSink properly handles lists of lists now

- BF: DataGrabber has option for raising Exception on getting empty lists

- BF: Traits logic for ‘requires’ metadata

- BF: allows workflows to be relocatable

- BF: nested workflows with connections don’t raise connection not found error

- BF: multiple workflows with identical nodenames and iterables do not create nestsed workflows

# Release 0.3.2 (Aug 03, 2010)

## Enhancements

> - all outputs from nodes are now pickled as part of workflow processing

> - added git developer docs

## Bugs fixed

- FreeSurfer

  - Fixed bugs in SegStats doctest

# Release 0.3.1 (Jul 29, 2010)

## Bugs fixed

- FreeSurfer

  - Fixed bugs in glmfit and concatenate

  - Added group t-test to freesurfer tutorial

# Release 0.3 (Jul 27, 2010)

## Incompatible changes

- Complete redesign of the Interface class - heavy use of Traits.

- Changes in the engine API - added Workflow and MapNode. Compulsory name argument.

## Features added

- General:

  - Type checking of inputs and outputs using Traits from ETS.

  - Support for nested workflows.

  - Preliminary Slicer and AFNI support.

  - New flexible DataGrabber node.

  - AtlasPick and Threshold nodes.

  - Preliminary support for XNAT.

  - Doubled number of the tutorials.

- FSL:

  - Added DTI processing nodes (note that TBSS nodes are still experimental).

  - Recreated FEAT workflow.

- SPM:

  - Added New Segment and many other nodes.

  - Redesigned second level analysis.