CHANGES

Upcoming release
================


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 miscelaneous 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 thorugh 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 miscelaneous 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 paramter 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.