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

# 1.7.0 (October 20, 2021)

(Full changelog)

> - FIX: Make ants.LaplacianThickness output_image a string, not file (https://github.com/nipy/nipype/pull/3393)

> - FIX: coord for mrconvert (https://github.com/nipy/nipype/pull/3369)

> - FIX: `antsRegistration` allows the `restrict_deformation` to be float (https://github.com/nipy/nipype/pull/3387)

> - FIX: Also allow errno.EBUSY during emptydirs on NFS (https://github.com/nipy/nipype/pull/3357)

> - FIX: Removed exists=True from MathsOutput (https://github.com/nipy/nipype/pull/3385)

> - FIX: Extension not extensions, after pybids v0.9 (https://github.com/nipy/nipype/pull/3380)

> - ENH: Add CAT12 SANLM denoising filter (https://github.com/nipy/nipype/pull/3374)

> - ENH: Add expected steps for FreeSurfer 7 recon-all (https://github.com/nipy/nipype/pull/3389)

> - ENH: Stop printing false positive differences when logging cached nodes (https://github.com/nipy/nipype/pull/3376)

> - ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform) (https://github.com/nipy/nipype/pull/3365)

> - ENH: `verbose` input should not be hashed in `ants.Registration` (https://github.com/nipy/nipype/pull/3377)

> - REF: Clean-up the BaseInterface `run()` function using context (https://github.com/nipy/nipype/pull/3347)

> - DOC: Fix typo in README (https://github.com/nipy/nipype/pull/3386)

> - STY: Make private member name consistent with the rest of them (https://github.com/nipy/nipype/pull/3346)

> - MNT: Simplify interface execution and better error handling of `Node` (https://github.com/nipy/nipype/pull/3349)

> - MNT: Add user name and email to Docker to appease git/annex/datalad (https://github.com/nipy/nipype/pull/3378)

> - CI: Update CircleCI machine image (https://github.com/nipy/nipype/pull/3391)

# 1.6.1 (June 16, 2021)

Bug-fix release in the 1.6.x series.

(Full changelog)

> - FIX: Set DistributedPluginBase.refidx type correctly (https://github.com/nipy/nipype/pull/3340)

> - FIX: change fsl interface randomise –f_only to –fonly for #3322 (https://github.com/nipy/nipype/pull/3325)

> - FIX: BET raising “No image files match: …” with very long file names (https://github.com/nipy/nipype/pull/3309)

> - FIX: Update SmoothEstimateOutputSpec resels description (https://github.com/nipy/nipype/pull/3316)

> - ENH: Adds interfaces for MRtrix utils shconv and sh2amp (https://github.com/nipy/nipype/pull/3280)

> - ENH: Interface for R (https://github.com/nipy/nipype/pull/3291)

> - ENH: Add CAT12 interfaces (https://github.com/nipy/nipype/pull/3310)

> - ENH: AFNI 3dNetCorr as afni.NetCorr (https://github.com/nipy/nipype/pull/3263)

> - ENH: Skip newline before Python call in batch submission to facilitate containerized runs (https://github.com/nipy/nipype/pull/3297)

> - ENH: Add new dwifslpreproc interface for MRtrix3 (https://github.com/nipy/nipype/pull/3278)

> - REF: Cache nodes in workflow to speed up construction, other optimizations (https://github.com/nipy/nipype/pull/3331)

> - DOC: Fixed Developer Setup Link in install.rst (https://github.com/nipy/nipype/pull/3330)

> - MNT: Blacklist Dipy 1.4.1 (https://github.com/nipy/nipype/pull/3335)

> - MNT: Drop support for numpy < 1.15.3 (https://github.com/nipy/nipype/pull/3284)

> - CI: Build docker images with Python 3.8 (https://github.com/nipy/nipype/pull/3287)

> - CI: Drop Circle doc builds (https://github.com/nipy/nipype/pull/3338)

> - CI: Drop Travis (https://github.com/nipy/nipype/pull/3332)

> - CI: Build docker images with Python 3.8 (https://github.com/nipy/nipype/pull/3287)

> - CI: Add specs and style checks (https://github.com/nipy/nipype/pull/3321)

> - CI: Move from Travis to GitHub actions (https://github.com/nipy/nipype/pull/3318)

# 1.6.0 (November 28, 2020)

New feature release in the 1.6.x series.

In addition to the usual bug fixes, significant reductions were made in workflow startup costs.

(Full changelog)

> - FIX: Canonicalize environment dicts to strings in Windows (https://github.com/nipy/nipype/pull/3267)

> - FIX: Purge deprecated exception content accesses (https://github.com/nipy/nipype/pull/3272)

> - FIX: Handle changes in CLI structure of mrtrix3.DWIBiasCorrect (https://github.com/nipy/nipype/pull/3248)

> - FIX: EpiReg changed to not list certain outputs when ‘wmseg’ input is specified (https://github.com/nipy/nipype/pull/3265)

> - FIX: CI issues (https://github.com/nipy/nipype/pull/3262)

> - FIX: SPM SliceTiming must accept either Int or float for ref_slice and sli… (https://github.com/nipy/nipype/pull/3255)

> - FIX: Raise version error when using `-g` with `antsAI` < 2.3.0 (https://github.com/nipy/nipype/pull/3256)

> - FIX: No longer depending on pydotplus (networkx >=2.0 update) (https://github.com/nipy/nipype/pull/3251)

> - FIX: ANTs’ utilities revision - bug fixes and add more operations to `ants.ImageMath` (https://github.com/nipy/nipype/pull/3236)

> - ENH: Handle unavailable traits due to version differences (https://github.com/nipy/nipype/pull/3273)

> - ENH: Optimize workflow.run performance (https://github.com/nipy/nipype/pull/3260)

> - DOC: Remove myself (@mr-c) from the zenodo metadata (https://github.com/nipy/nipype/pull/3271)

# 1.5.1 (August 16, 2020)

Bug-fix release in the 1.5.x series.

This release includes small updates to ANTs utilities that lie somewhere between bug fixes and enhancements.

(Full changelog)

> - FIX: Warn for min/max_ver traits when tool version can’t be parsed (https://github.com/nipy/nipype/pull/3241)

> - FIX: Serialize all interface arguments when exporting workflows (https://github.com/nipy/nipype/pull/3240)

> - FIX: Permit identity transforms in list of transforms given to ants.ApplyTransforms (https://github.com/nipy/nipype/pull/3237)

> - FIX: ANTs’ utilities revision - bug fixes and add more operations to `ants.ImageMath` (https://github.com/nipy/nipype/pull/3236)

> - DOC: Skip BIDSDataGrabber doctest if pybids is missing (https://github.com/nipy/nipype/pull/3224)

# 1.5.0 (June 03, 2020)

New feature release in the 1.5.x series.

In this release, the example scripts have been split out into their own package: niflow-nipype1-examples.

(Full changelog)

> - FIX: volterra_expansion_order documentation error (https://github.com/nipy/nipype/pull/3213)

> - FIX: BET incorrect output paths (https://github.com/nipy/nipype/pull/3214)

> - FIX: Terminal output in `report.rst` spreads one line per character (https://github.com/nipy/nipype/pull/3220)

> - FIX: Allow parsing freesurfer 7 version string (https://github.com/nipy/nipype/pull/3216)

> - FIX: Use PackageInfo to get NiftyReg version (https://github.com/nipy/nipype/pull/3194)

> - FIX: Partial rollback of N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3188)

> - FIX: ANTs’ tools maintenance overhaul (https://github.com/nipy/nipype/pull/3180)

> - FIX: load_resultfile crashes if open resultsfile from crashed job (https://github.com/nipy/nipype/pull/3182)

> - FIX: FSL model.py make multiple F-tests (https://github.com/nipy/nipype/pull/3166)

> - ENH: Restore ants.legacy interfaces (https://github.com/nipy/nipype/pull/3222)

> - ENH: Add `"TruncateImageIntensity"` operation to `ants.utils.Image.Math` (https://github.com/nipy/nipype/pull/3210)

> - ENH: SPM NewSegment multi-channel segmentation (https://github.com/nipy/nipype/pull/3162)

> - ENH: Add reverse-ordered transform lists to ants.Registration outputs (https://github.com/nipy/nipype/pull/3192)

> - ENH: Improve workflow connect performance (https://github.com/nipy/nipype/pull/3184)

> - ENH: Add `ConstrainedSphericalDeconvolution` interface to replace `EstimateFOD` for MRtrix3’s `dwi2fod` (https://github.com/nipy/nipype/pull/3176)

> - ENH: Detect values for EulerNumber interface (https://github.com/nipy/nipype/pull/3173)

> - ENH: Remove examples from repository (https://github.com/nipy/nipype/pull/3172)

> - TEST: Clean up tests (https://github.com/nipy/nipype/pull/3195)

> - TEST: Mock terminal output before testing changing default value (https://github.com/nipy/nipype/pull/3193)

> - REF: make invocations of python and pytest consistent with the one used/desired python (https://github.com/nipy/nipype/pull/3208)

> - REF: Prefer math.gcd to hand-rolled Euclid’s algorithm (https://github.com/nipy/nipype/pull/3177)

> - REF: Removed all uses of numpy_mmap (https://github.com/nipy/nipype/pull/3121)

> - DOC: Sphinx 3 compatibility (https://github.com/nipy/nipype/pull/3206)

> - DOC: Update links, typos in contributing guide (https://github.com/nipy/nipype/pull/3160)

> - DOC: Update SelectFiles docstring to match actual behavior (https://github.com/nipy/nipype/pull/3041)

> - DOC: Updated .zenodo.json file (https://github.com/nipy/nipype/pull/3167)

> - DOC: Update .zenodo.json (https://github.com/nipy/nipype/pull/3165)

> - MNT: Permit recent nilearns (https://github.com/nipy/nipype/pull/2841)

> - MNT: Test Python 3.8 (https://github.com/nipy/nipype/pull/3154)

> - MNT: Restore ReadTheDocs (https://github.com/nipy/nipype/pull/3207)

> - MNT: Update Zenodo ordering based on commit count (https://github.com/nipy/nipype/pull/3169)

# 1.4.2 (February 14, 2020)

(Full changelog)

> - FIX: Allow `fsl.MultipleRegressDesign` to create multiple F-tests (https://github.com/nipy/nipype/pull/3166)

> - FIX: Reliably parse SGE job IDs in the presence of warnings (https://github.com/nipy/nipype/pull/3168)

> - FIX: Move TraitType import, handle API change for NoDefaultSpecified (https://github.com/nipy/nipype/pull/3159)

# 1.4.1 (January 27, 2020)

(Full changelog)

> - FIX: DataSink to S3 buckets (https://github.com/nipy/nipype/pull/3130)

> - FIX: improve version checking for nodes of workflows (https://github.com/nipy/nipype/pull/3152)

> - FIX: mapnode to generate result file when crashes in single node mode (https://github.com/nipy/nipype/pull/3143)

> - FIX: Can’t seem to import workflows from niflows in CircleCI (https://github.com/nipy/nipype/pull/3134)

> - FIX: Repair aftermath of docs refactor (https://github.com/nipy/nipype/pull/3133)

> - FIX: change ANTS number_of_time_steps from Float to Int (https://github.com/nipy/nipype/pull/3118)

> - DOC: Revise generation of examples to work in RTD (https://github.com/nipy/nipype/pull/3132)

> - DOC: Bring examples generation back to `doc/conf.py` (https://github.com/nipy/nipype/pull/3131)

> - DOC: Documentation overhaul (https://github.com/nipy/nipype/pull/3124)

> - DOC: Deep revision of documentation building (https://github.com/nipy/nipype/pull/3120)

> - DOC: Deduplicate code for Sphinx’s APIdoc generation (https://github.com/nipy/nipype/pull/3119)

> - MNT: Update requirements.txt post-1.4 (https://github.com/nipy/nipype/pull/3153)

# 1.4.0 (December 20, 2019)

(Full changelog)

> - FIX: Mark strings containing regex escapes as raw (https://github.com/nipy/nipype/pull/3106)

> - ENH: Pacify DeprecationWarnings caused by nibabel 3 pre-release (https://github.com/nipy/nipype/pull/3099)

> - ENH: Allow Nipype configuration directory to be specified with NIPYPE_CONFIG_DIR environment variable (https://github.com/nipy/nipype/pull/3073)

> - ENH: Add options and outputs to `fsl.Eddy` interface (https://github.com/nipy/nipype/pull/3034)

> - ENH: Add skull_file output to fsl.BET interface (https://github.com/nipy/nipype/pull/3095)

> - RF: Drop various remaining compatibilities for Python < 3.5 (https://github.com/nipy/nipype/pull/2831)

> - DOC: Add Python 2 statement to README, reference maintenance branch in CONTRIBUTING (https://github.com/nipy/nipype/pull/3115)

> - DOC: Miss underline before cmd in example code (https://github.com/nipy/nipype/pull/3107)

> - STY: Black (https://github.com/nipy/nipype/pull/3096)

> - MNT: Set junit_family to suppress pytest warning (https://github.com/nipy/nipype/pull/3111)

> - MNT: Fix Dorota Jarecka ORCID (https://github.com/nipy/nipype/pull/3100)

> - MNT: Drop Python 2 support (https://github.com/nipy/nipype/pull/2654)

# 1.3.1 (November 12, 2019)

> - FIX: Restore checking traits or bunch (https://github.com/nipy/nipype/pull/3094)

# 1.3.0 (November 11, 2019)

(Full changelog)

> - FIX: Fixed typo in QwarpInputSpec Trait description (https://github.com/nipy/nipype/pull/3079)

> - FIX: Restore `AFNICommand._get_fname`, required by some interfaces (https://github.com/nipy/nipype/pull/3071)

> - FIX: Remove asynchronous chdir callback (https://github.com/nipy/nipype/pull/3060)

> - FIX: Minimize scope for directory changes while loading results file (https://github.com/nipy/nipype/pull/3061)

> - ENH: Minimize the number of calls to `_load_results` when populating inputs (https://github.com/nipy/nipype/pull/3075)

> - ENH: Refactor savepkl/loadpkl - add a window for loadpkl to wait for the file (https://github.com/nipy/nipype/pull/3089)

> - ENH: Add “ExportFile” interface as simple alternative to “DataSink” (https://github.com/nipy/nipype/pull/3054)

> - ENH: Allow nipype.cfg in cwd to be read even if ~/.nipype does not exist (https://github.com/nipy/nipype/pull/3072)

> - ENH: Add precommit information for contributors and pre-commit style (https://github.com/nipy/nipype/pull/3063)

> - ENH: Delay etelemetry for non-interactive sessions, report bad versions (https://github.com/nipy/nipype/pull/3049)

> - ENH: Run memoized check_version at REPL import, Node/Workflow/Interface init (https://github.com/nipy/nipype/pull/30)

> - RF: Provide functions to augment old Path.mkdir, Path.resolve methods (https://github.com/nipy/nipype/pull/3050)

> - RF: Redirect nipype.workflows to niflow.nipype1.workflows (https://github.com/nipy/nipype/pull/3067)

> - TST: Skip dcm2niix test if data fails to download (https://github.com/nipy/nipype/pull/3059)

> - TST: dcm2niix test fix (https://github.com/nipy/nipype/pull/3058)

> - MAINT: Drop Python 3.4 support (https://github.com/nipy/nipype/pull/3062)

> - CI: `make specs` on Travis (https://github.com/nipy/nipype/pull/3066)

# 1.2.3 (September 23, 2019)

Python 1.2.3 will be the last version to support Python 3.4.

(Full changelog)

> - FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037)

> - FIX: Drop deprecated message argument to `FileNotFoundError` (https://github.com/nipy/nipype/pull/3035)

> - FIX: Handle NIFTI extensions in `afni.Qwarp` (https://github.com/nipy/nipype/pull/3028)

> - FIX: Disallow returning `None` in `pipeline.utils.load_resultfile` (https://github.com/nipy/nipype/pull/3023)

> - ENH: Allow afni.CatMatvec to accept empty string opkeys (https://github.com/nipy/nipype/pull/2943)

> - ENH: Add `mrrtrix3.MRResize` interface (https://github.com/nipy/nipype/pull/3031)

> - ENH: Add version check / telemetry to Nipype (https://github.com/nipy/nipype/pull/3027)

> - ENH: Update MCFLIRT outputs for FSL 6+ (https://github.com/nipy/nipype/pull/3029)

> - ENH: Lightweight node cache checking (https://github.com/nipy/nipype/pull/3026)

> - ENH: Avoid loading result from file when writing reports (https://github.com/nipy/nipype/pull/3024)

> - ENH: replace portalocker with filelock (https://github.com/nipy/nipype/pull/3025)

> - MAINT: Set minimum yapf for checkspecs to 0.27 (https://github.com/nipy/nipype/pull/3033)

# 1.2.2 (September 07, 2019)

(Full changelog)

> - FIX: Ensure `loadpkl` returns a not None value (https://github.com/nipy/nipype/pull/3020)

> - FIX: `loadpkl` failed when pklz file contained versioning info (https://github.com/nipy/nipype/pull/3017)

> - FIX: Update mne.WatershedBEM command line (https://github.com/nipy/nipype/pull/3007)

> - FIX: Specify correct stop criterion flag in PETPVC (https://github.com/nipy/nipype/pull/3010)

> - ENH: Add interface for AFNI `3dTsmooth` (https://github.com/nipy/nipype/pull/2948)

> - ENH: Additional arguments to ANTs N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3012)

> - ENH: Add `--rescale-intensities` and name_source to N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/3011)

> - ENH: Add index_mask_file input to ImageStats (https://github.com/nipy/nipype/pull/3005)

> - RF: Remove versioning from `loadpkl` (https://github.com/nipy/nipype/pull/3019)

> - MAINT: Add `python_requires` to package metadata (https://github.com/nipy/nipype/pull/3006)

# 1.2.1 (August 19, 2019)

(Full changelog)

> - FIX: Resolve/rebase paths from/to results files (https://github.com/nipy/nipype/pull/2971)

> - FIX: Use `load_resultfile` when loading a results pickle (https://github.com/nipy/nipype/pull/2985)

> - FIX: Incorrect extension identified when checking `File` traits (https://github.com/nipy/nipype/pull/2987)

> - FIX: Correctly pickle `OuputMultiObject` traits (https://github.com/nipy/nipype/pull/2983)

> - FIX: Improve output handling in DWIDenoise and DWIBiasCorrect (https://github.com/nipy/nipype/pull/2978)

> - FIX: Docker build (https://github.com/nipy/nipype/pull/2963)

> - FIX: Remove ‘=’ signs from EddyQuad argument specifications (https://github.com/nipy/nipype/pull/2941)

> - FIX: Set input model to bedpostx for camino.TrackBedpostxProba (https://github.com/nipy/nipype/pull/2947)

> - FIX: Allow `max_sh` to not be set (auto mode) (https://github.com/nipy/nipype/pull/2940)

> - ENH: Update mrtrix reconst.py EstimateFOD max_sh to be able to accept list (https://github.com/nipy/nipype/pull/2990)

> - ENH: Let `indirectory` handle `nipype.utils.filemanip.Path` (https://github.com/nipy/nipype/pull/2989)

> - ENH: Add resolve/rebase `BasePath` traits methods & tests (https://github.com/nipy/nipype/pull/2970)

> - ENH: Modify `Directory` and `File` traits to get along with pathlib (https://github.com/nipy/nipype/pull/2962)

> - REF: Update nipype2boutiques script (https://github.com/nipy/nipype/pull/2894)

> - TST: Parametrize JoinNode expansion tests over config `needed_outputs` (https://github.com/nipy/nipype/pull/2981)

> - MAINT: Pin lxml<4.4.0 for Python 3.4 (https://github.com/nipy/nipype/pull/2980)

> - MAINT: Refactor `aggregate_outputs` for readability (https://github.com/nipy/nipype/pull/2969)

> - MAINT: Bump neurodocker version (https://github.com/nipy/nipype/pull/2965)

> - MAINT: Various minor improvements to complement previous PR (https://github.com/nipy/nipype/pull/2964)

> - MAINT: Sort dependencies alphabetically (https://github.com/nipy/nipype/pull/2961)

# 1.2.0 (May 09, 2019)

(Full changelog)

> - FIX: Parsing of filename in AlignEpiAnatPy when filename does not have + (https://github.com/nipy/nipype/pull/2909)

> - FIX: Import nibabel reorientation bug fix (https://github.com/nipy/nipype/pull/2912)

> - FIX: Update FNIRT outputs for warped_file log_file to include cwd (https://github.com/nipy/nipype/pull/2900)

> - FIX: Sort conditions in bids_gen_info to ensure consistent order (https://github.com/nipy/nipype/pull/2867)

> - FIX: Some traits-5.0.0 don’t work with Python 2.7 (https://github.com/nipy/nipype/pull/1)

> - ENH: CompCor enhancement (https://github.com/nipy/nipype/pull/2878)

> - ENH: Do not override caught exceptions with FileNotFoundError from unfinished hashfile (https://github.com/nipy/nipype/pull/2919)

> - ENH: More verbose description when a faulty results file is loaded (https://github.com/nipy/nipype/pull/2920)

> - ENH: Add all DIPY workflows dynamically (https://github.com/nipy/nipype/pull/2905)

> - ENH: Add mrdegibbs and dwibiascorrect from mrtrix3 (https://github.com/nipy/nipype/pull/2904)

> - TEST: Fix CI builds (https://github.com/nipy/nipype/pull/2927)

> - MAINT: Reduce deprecation warnings (https://github.com/nipy/nipype/pull/2903)

# 1.1.9 (February 25, 2019)

(Full changelog)

> - FIX: Make positional arguments to LaplacianThickness require previous argument (https://github.com/nipy/nipype/pull/2848)

> - FIX: Import math and csv modules for bids_gen_info (https://github.com/nipy/nipype/pull/2881)

> - FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (https://github.com/nipy/nipype/pull/2739)

> - ENH: Allow afni.MaskTool to take multiple input files (https://github.com/nipy/nipype/pull/2892)

> - ENH: Add flags dictionary input to spm.Level1Design (https://github.com/nipy/nipype/pull/2861)

> - ENH: Threshold stddev once only in TSNR (https://github.com/nipy/nipype/pull/2883)

> - ENH: Add workbench.CiftiSmooth interface (https://github.com/nipy/nipype/pull/2871)

> - DOC: Replace initialism typo in comment with intended phrase (https://github.com/nipy/nipype/pull/2875)

> - DOC: Fix typos in ANTs Registration input documentation (https://github.com/nipy/nipype/pull/2869)

# 1.1.8 (January 28, 2019)

(Full changelog)

> - FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)

> - FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)

> - ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)

> - ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)

> - ENH: Add FSL eddy_quad interface (https://github.com/nipy/nipype/pull/2825)

> - ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)

> - ENH: Support for BIDS event files (https://github.com/nipy/nipype/pull/2845)

> - ENH: CompositeTransformUtil, new ANTs interface (https://github.com/nipy/nipype/pull/2785)

> - RF: Move pytest and pytest-xdist from general requirement into tests_required (https://github.com/nipy/nipype/pull/2850)

> - DOC: Add S3DataGrabber example (https://github.com/nipy/nipype/pull/2849)

> - DOC: Skip conftest module in API generation (https://github.com/nipy/nipype/pull/2852)

> - DOC: Hyperlink DOIs to preferred resolver (https://github.com/nipy/nipype/pull/2833)

> - MAINT: Install numpy!=1.16.0 from conda in Docker (https://github.com/nipy/nipype/pull/2862)

> - MAINT: Drop pytest-xdist requirement, minimum pytest version (https://github.com/nipy/nipype/pull/2856)

> - MAINT: Disable numpy 1.16.0 for Py2.7 (https://github.com/nipy/nipype/pull/2855)

# 1.1.7 (December 17, 2018)

(Full changelog)

> - FIX: Copy node list before generating a flat graph (https://github.com/nipy/nipype/pull/2828)

> - FIX: Update pytest req’d version to 3.6 (https://github.com/nipy/nipype/pull/2827)

> - FIX: Set ResourceMonitor.fname to an absolute path (https://github.com/nipy/nipype/pull/2824)

> - FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected) (https://github.com/nipy/nipype/pull/2817)

> - FIX: Indices were swapped for memory and cpu profile data (https://github.com/nipy/nipype/pull/2816)

> - FIX: `status_callback` not called with `stop_on_first_crash` (https://github.com/nipy/nipype/pull/2810)

> - FIX: Change undefined ScriptError on LFS plugin to IOError (https://github.com/nipy/nipype/pull/2803)

> - ENH: Add NaN failure mode to CompCor interfaces (https://github.com/nipy/nipype/pull/2819)

> - ENH: Enable cnr_maps and residuals outputs for FSL eddy (https://github.com/nipy/nipype/pull/2750)

> - ENH: Improve `str2bool` + doctests (https://github.com/nipy/nipype/pull/2807)

> - TST: Improve py.test configuration of doctests (https://github.com/nipy/nipype/pull/2802)

> - DOC: Update DOI badge to point to all versions (https://github.com/nipy/nipype/pull/2804)

> - MAINT: Offload interfaces with help formatting (https://github.com/nipy/nipype/pull/2797)

> - MAINT: Reduce minimal code redundancy in filemanip.get_dependencies (https://github.com/nipy/nipype/pull/2782)

> - MAINT: Delayed imports to reduce import time (https://github.com/nipy/nipype/pull/2809)

# 1.1.6 (November 26, 2018)

(Full changelog)

> - FIX: MapNodes fail when `MultiProcPlugin` passed by instance (https://github.com/nipy/nipype/pull/2786)

> - FIX: –fineTune arguments order for MeshFix command (https://github.com/nipy/nipype/pull/2780)

> - ENH: Add mp_context plugin arg for MultiProc (https://github.com/nipy/nipype/pull/2778)

> - ENH: Create a crashfile even if ‘stop_on_first_crash’ is set (https://github.com/nipy/nipype/pull/2774)

> - ENH: Add ExtractedBrainN4 output to ANTs CorticalThickness interface (https://github.com/nipy/nipype/pull/2784)

> - STY: Combine split import (https://github.com/nipy/nipype/pull/2801)

> - DOC: use https in css stylesheet url (https://github.com/nipy/nipype/pull/2779)

> - MAINT: Outsource `get_filecopy_info()` from interfaces (https://github.com/nipy/nipype/pull/2798)

> - MAINT: Import only Sequence to avoid DeprecationWarning (https://github.com/nipy/nipype/pull/2793)

> - MAINT: One less DeprecationWarning (configparser) (https://github.com/nipy/nipype/pull/2794)

> - MAINT: DeprecationWarning: use `HasTraits.trait_set` instead (https://github.com/nipy/nipype/pull/2792)

> - MAINT: Stop using deprecated `logger.warn()` (https://github.com/nipy/nipype/pull/2788)

> - MAINT: Move `interfaces.base.run_command` to `nipype.utils.subprocess` (https://github.com/nipy/nipype/pull/2777)

> - MAINT: Force numpy>=1.15.4 when Python>=3.7 (https://github.com/nipy/nipype/pull/2775)

# 1.1.5 (November 08, 2018)

Hotfix release.

(Full changelog)

> - ENH: Allow timeouts during SLURM job status checks (https://github.com/nipy/nipype/pull/2767)

> - RF: Subclass non-daemon variants of all multiprocessing contexts (https://github.com/nipy/nipype/pull/2771)

# 1.1.4 (October 31, 2018)

(Full changelog)

> - FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754)

> - FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757)

> - FIX: Refine FSL.split output identification (https://github.com/nipy/nipype/pull/2746)

> - FIX: Reuse _gen_filename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734)

> - FIX: Remove ‘reg_term’ default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731)

> - FIX: Keep profile files when `remove_unnecessary_outputs = true` (https://github.com/nipy/nipype/pull/2718)

> - ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (https://github.com/nipy/nipype/pull/2740)

> - ENH: Add compression option for bru2nii (https://github.com/nipy/nipype/pull/2762)

> - ENH: Add slice_encoding_direction input to TShift (https://github.com/nipy/nipype/pull/2753)

> - ENH: Add ‘sse’ output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749)

> - ENH: Update `ants.LaplacianThickness` to use `name_source` (https://github.com/nipy/nipype/pull/2747)

> - ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735)

> - ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725)

> - TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730)

> - DOC: Move user docs from nipype to nipype_tutorial (https://github.com/nipy/nipype/pull/2726)

> - DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758)

> - MAINT: Use neurodocker 0.4.1 + apt install afni (https://github.com/nipy/nipype/pull/2707)

> - MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701)

> - MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723)

> - MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728)

> - CI: Lock travis pybids 0.6.5 (https://github.com/nipy/nipype/pull/2720)

# 1.1.3 (September 24, 2018)

(Full changelog)

> - FIX: Return afni.Qwarp outputs as absolute paths (https://github.com/nipy/nipype/pull/2705)

> - FIX: Add informative error for interfaces that fail to return valid runtime object (https://github.com/nipy/nipype/pull/2692)

> - FIX: Construct MCFLIRT output paths relative to out_file (https://github.com/nipy/nipype/pull/2703)

> - FIX: SLURM plugin polling (https://github.com/nipy/nipype/pull/2693)

> - FIX: Handle missing substring in SPM docs (https://github.com/nipy/nipype/pull/2691)

> - ENH: Add colorFA output to DIPY DTI interface (https://github.com/nipy/nipype/pull/2695)

> - RF: Use runtime.cwd in Rename (https://github.com/nipy/nipype/pull/2688)

> - DOC: Fix naming of motion parameters (roll/yaw swapped) (https://github.com/nipy/nipype/pull/2696)

> - DOC: Update links to user and developer help forums (https://github.com/nipy/nipype/pull/2686)

> - CI: Test 3.7, resume testing nipy extras (https://github.com/nipy/nipype/pull/2682)

# 1.1.2 (August 11, 2018)

Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.

(Full changelog)

> - FIX: Read BIDS config.json under grabbids or layout (https://github.com/nipy/nipype/pull/2679)

> - FIX: Node __repr__ and detailed graph expansion (https://github.com/nipy/nipype/pull/2669)

> - FIX: Prevent double-collapsing of nested lists by OutputMultiObject (https://github.com/nipy/nipype/pull/2673)

> - ENH: Add interface to SPM realign_unwarp (https://github.com/nipy/nipype/pull/2635)

> - MAINT: Fix wheel build to ensure futures is only required in Python 2 (https://github.com/nipy/nipype/pull/2678)

> - MAINT: ensure interface _cmd only includes executable (https://github.com/nipy/nipype/pull/2674)

> - MAINT: Issue template: Pretty print platform details (https://github.com/nipy/nipype/pull/2671)

> - CI: removing travis_retry for pip install pytest xdist 1.22.5 (https://github.com/nipy/nipype/pull/2664)

# 1.1.1 (July 30, 2018)

(Full changelog)

> - FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637)

> - FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656)

> - FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651)

> - FIX: changing Node._output_dir to realpath (https://github.com/nipy/nipype/pull/2639)

> - FIX: Typo in DWIExtract of Mrtrix3interface (https://github.com/nipy/nipype/pull/2634)

> - FIX: Typo in FSLXCommandInputSpec (https://github.com/nipy/nipype/pull/2628)

> - ENH: Allow transform to be saved from AFNI 3dWarp (https://github.com/nipy/nipype/pull/2642)

> - ENH: Allow BIDS-style slice timings to be passed directly to TShift (https://github.com/nipy/nipype/pull/2608)

> - ENH: S3 access using instance role (https://github.com/nipy/nipype/pull/2621)

> - ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636)

> - TEST: make specs (https://github.com/nipy/nipype/pull/2653)

> - DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647)

> - MAINT: Remove vestiges of nose testing library (https://github.com/nipy/nipype/pull/2662)

> - MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649)

> - CI: Install pytest>=3.4 in Travis (https://github.com/nipy/nipype/pull/2659)

# 1.1.0 (July 04, 2018)

(Full changelog)

> - RF: Futures-based MultiProc (https://github.com/nipy/nipype/pull/2598)

> - FIX: Avoid closing file descriptors on Windows (https://github.com/nipy/nipype/pull/2617)

> - MAINT: Play nice with external logging (https://github.com/nipy/nipype/pull/2611)

> - MAINT: Remove ignore_exception and terminal_output traits from input specs (https://github.com/nipy/nipype/pull/2618)

> - MAINT: Converge autotest names (https://github.com/nipy/nipype/pull/2610)

> - ENH: Add versioning metadata to crash files (https://github.com/nipy/nipype/pull/2626)

> - ENH add -dsort option to TProject (https://github.com/nipy/nipype/pull/2623)

> - ENH: Add Rescale interface (https://github.com/nipy/nipype/pull/2599)

> - DOC: Improve documentation for ANTs/FSL interfaces (https://github.com/nipy/nipype/pull/2593)

> - CI: Stop using Miniconda on Travis (https://github.com/nipy/nipype/pull/2600)

> - CI: Add PyPI validation on rel/* branches (https://github.com/nipy/nipype/pull/2603)

# 1.0.4 (May 29, 2018)

(Full changelog)

> - FIX: Update logging levels in enable_debug_mode (https://github.com/nipy/nipype/pull/2595)

> - FIX: Set default result in DistributedPluginBase._clean_queue (https://github.com/nipy/nipype/pull/2596)

> - FIX: Correctly connect JoinNodes in nested iterables (https://github.com/nipy/nipype/pull/2597)

> - FIX: DTITK nonlinear workflow origin reslicing (https://github.com/nipy/nipype/pull/2561)

> - FIX: ResponseSD support for multiple b-vals (https://github.com/nipy/nipype/pull/2582)

> - FIX: Workaround to ICA-AROMA change of directory (https://github.com/nipy/nipype/pull/2566)

> - FIX/TEST: Gunzip cleanup and test (https://github.com/nipy/nipype/pull/2564)

> - FIX: Print UID in crashfile if login name is unavailable (https://github.com/nipy/nipype/pull/2563)

> - ENH: initial connectome workbench support (https://github.com/nipy/nipype/pull/2594)

> - ENH: AFNI (3d)LocalBistat interface (https://github.com/nipy/nipype/pull/2590)

> - ENH: Reorient interface (https://github.com/nipy/nipype/pull/2572)

> - ENH: FSL slice interface (https://github.com/nipy/nipype/pull/2585)

> - ENH: LabelGeometryMeasures interface (https://github.com/nipy/nipype/pull/2586)

> - ENH: MRTrix3 dwidenoise interface (https://github.com/nipy/nipype/pull/2568)

> - ENH: ReportCapableInterface mix-in/base interface (https://github.com/nipy/nipype/pull/2560)

> - CI: Move PyPI deployment to Circle (https://github.com/nipy/nipype/pull/2587)

> - CI: Submit Travis results to codecov (https://github.com/nipy/nipype/pull/2574)

# 1.0.3 (April 30, 2018)

(Full changelog)

> - FIX: Propagate explicit Workflow config to Nodes (https://github.com/nipy/nipype/pull/2559)

> - FIX: Return non-enhanced volumes from dwi_flirt (https://github.com/nipy/nipype/pull/2547)

> - FIX: Skip filename generation when required fields are missing (https://github.com/nipy/nipype/pull/2549)

> - FIX: Fix Afni’s Allineate hashing and out_file (https://github.com/nipy/nipype/pull/2502)

> - FIX: Replace deprecated `HasTraits.get` with `trait_get` (https://github.com/nipy/nipype/pull/2534)

> - FIX: Typo in “antsRegistrationSyNQuick.sh” (https://github.com/nipy/nipype/pull/2544)

> - FIX: DTITK Interface (https://github.com/nipy/nipype/pull/2514)

> - FIX: Add `-mas` argument to fsl.utils.ImageMaths (https://github.com/nipy/nipype/pull/2529)

> - FIX: Build cmdline from working directory (https://github.com/nipy/nipype/pull/2521)

> - FIX: FSL orthogonalization bug (https://github.com/nipy/nipype/pull/2523)

> - FIX: Re-enable dcm2niix source_names (https://github.com/nipy/nipype/pull/2550)

> - ENH: Add an activation count map interface (https://github.com/nipy/nipype/pull/2522)

> - ENH: Revise the implementation of FuzzyOverlap (https://github.com/nipy/nipype/pull/2530)

> - ENH: Add MultiObject, ensure/simplify_list; alias old names for 1.x compatibility (https://github.com/nipy/nipype/pull/2517)

> - ENH: Add LibraryBaseInterface (https://github.com/nipy/nipype/pull/2538)

> - ENH: Define default output file template for afni.CatMatvec (https://github.com/nipy/nipype/pull/2527)

> - MAINT: Deprecate terminal_output and ignore_exception from CommandLine (https://github.com/nipy/nipype/pull/2552)

> - MAINT: Set traits default values properly (https://github.com/nipy/nipype/pull/2533)

> - MAINT: use RawConfigParser (https://github.com/nipy/nipype/pull/2542)

> - MAINT: Minor autotest cleanups (https://github.com/nipy/nipype/pull/2519)

> - CI: Add retry script for Docker commands (https://github.com/nipy/nipype/pull/2516)

# 1.0.2 (March 27, 2018)

(Full changelog)

> - FIX: dcm2niix interface (https://github.com/nipy/nipype/pull/2498)

> - FIX: mark .niml.dset as special extension in utils.filemanip (https://github.com/nipy/nipype/pull/2495)

> - FIX: handle automatic module creation, name extraction, default value (https://github.com/nipy/nipype/pull/2490)

> - FIX: Check and report mount table parsing failures (https://github.com/nipy/nipype/pull/2476)

> - FIX: Check against full node name when reconnecting JoinNodes (https://github.com/nipy/nipype/pull/2479)

> - DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503

> - DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482)

> - DOC: Describe ‘orphaned’ tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481)

> - DOC: Add details for dcm2niix output filename pattern (https://github.com/nipy/nipype/pull/2512)

> - ENH: Add interface for AFNI 3dNwarpAdjust (https://github.com/nipy/nipype/pull/2450)

> - ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104)

> - ENH: Add interpolation order parameter to NiftyReg’s RegTools (https://github.com/nipy/nipype/pull/2471)

> - MAINT: Stray warnings and exceptions (https://github.com/nipy/nipype/pull/2478)

> - MAINT: Add dev install option, update CONTRIBUTING (https://github.com/nipy/nipype/pull/2477)

> - MAINT: Sync requirements with info.py (https://github.com/nipy/nipype/pull/2472)

> - CI: Update Travis builds, Docker to use latest miniconda (https://github.com/nipy/nipype/pull/2455)

> - TEST: Parallelize pytest (https://github.com/nipy/nipype/pull/2469)

# 1.0.1 (February 27, 2018)

(Full changelog)

- FIX: Small bug in freesurfer label2annot fill_thresh specs [#2377](https://github.com/nipy/nipype/pull/2377)

- FIX: Error creating gradients in DTIRecon [#2460](https://github.com/nipy/nipype/pull/2460)

- FIX: improve matlab_cmd [#2452](https://github.com/nipy/nipype/pull/2452)

- FIX: Extract unit information from image header in CompCor [#2458](https://github.com/nipy/nipype/pull/2458)

- FIX: Update pybids data directory, unbundle out-of-date numpydoc [#2437](https://github.com/nipy/nipype/pull/2437)

- FIX: Out_file bugs in Afni.Zcat and Afni.Merge interfaces [#2424](https://github.com/nipy/nipype/pull/2424)

- FIX: Re-enable spm.Realign to take lists of lists of files [#2409](https://github.com/nipy/nipype/pull/2409)

- FIX: Remove deprecated output from ICC interface [#2422](https://github.com/nipy/nipype/pull/2422)

- FIX: Argstr for mask in Afni.BlurToFWHM [#2418](https://github.com/nipy/nipype/pull/2418)

- FIX: Default value for sbatch_args (SLURMGraph) [#2417](https://github.com/nipy/nipype/pull/2417)

- FIX: Ortvec argstr for Afni.Deconvolve [#2415](https://github.com/nipy/nipype/pull/2415)

- FIX: Bug fixes for afni.model [#2398](https://github.com/nipy/nipype/pull/2398)

- DOC: Add brief neurodocker tutorial [#2464](https://github.com/nipy/nipype/pull/2464)

- DOC: Fix tutorials [#2459](https://github.com/nipy/nipype/pull/2459)

- ENH: antsRegistrationSyNQuick interface [#2453](https://github.com/nipy/nipype/pull/2453)

- ENH: Automate updates of CHANGES [#2440](https://github.com/nipy/nipype/pull/2440)

- ENH: Add SPM Fieldmap Tool wrapper [#1905](https://github.com/nipy/nipype/pull/1905)

- ENH: Additional option for DataGrabber [#1915](https://github.com/nipy/nipype/pull/1915)

- ENH: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve [#2426](https://github.com/nipy/nipype/pull/2426)

- ENH: c3d/c4d interface [#2430](https://github.com/nipy/nipype/pull/2430)

- ENH: Allow input weight for AFNI’s volreg. [#2396](https://github.com/nipy/nipype/pull/2396)

- ENH: Delay crashing if exception is raised in local hash check [#2410](https://github.com/nipy/nipype/pull/2410)

- CI: Add doctests to pytest script [#2449](https://github.com/nipy/nipype/pull/2449)

- CI: Ignore tests in calculating coverage [#2443](https://github.com/nipy/nipype/pull/2443)

- CI: Saturate Circle workflow [#2386](https://github.com/nipy/nipype/pull/2386)

- REF: Update and factor mount table parsing [#2444](https://github.com/nipy/nipype/pull/2444)

- REF: Make ignore_exception a class attribute [#2414](https://github.com/nipy/nipype/pull/2414)

# 1.0.0 (January 24, 2018)

(Full changelog)

- FIX: Change to interface workdir within `Interface.run()` instead Node (https://github.com/nipy/nipype/pull/2384)

- FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344)

- FIX: Graph plugins submissions (https://github.com/nipy/nipype/pull/2359)

- FIX: Logging error if % in interface command (https://github.com/nipy/nipype/pull/2364)

- FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373)

- FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369)

- FIX: Errors parsing `$DISPLAY` (https://github.com/nipy/nipype/pull/2363)

- FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/nipype/pull/2368)

- FIX: Explicitly collect MultiProc job IDs (https://github.com/nipy/nipype/pull/2378)

- FIX: Correct Windows environment canonicalization (https://github.com/nipy/nipype/pull/2328)

- FIX: Linked libraries (https://github.com/nipy/nipype/pull/2322)

- REF+FIX: Move BIDSDataGrabber to interfaces.io + fix correct default behavior (https://github.com/nipy/nipype/pull/2336)

- REF+MAINT: Simplify hashing (https://github.com/nipy/nipype/pull/2383)

- MAINT: Cleanup Interfaces base (https://github.com/nipy/nipype/pull/2387)

- MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376)

- MAINT: Cleaning / simplify `Node` (https://github.com/nipy/nipype/pull/2325)

- MAINT+ENH: Update and extend MRtrix3 interfaces (https://github.com/nipy/nipype/pull/2338)

- ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337)

- ENH: Allow specific interface command prefixes (https://github.com/nipy/nipype/pull/2379)

- STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358)

- STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355)

- STY: Apply yapf to codebase (https://github.com/nipy/nipype/pull/2371)

- DOC: Updated guide for contributing (https://github.com/nipy/nipype/pull/2393)