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# Changes in Nipype

## 1.9.2 (December 17, 2024)

Bug fix release in the 1.9.x series.

> - FIX: Missed np.savetxt bstring (https://github.com/nipy/nipype/pull/3704)

> - MAINT: Bump astral-sh/setup-uv from 3 to 4 (https://github.com/nipy/nipype/pull/3702)

> - MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3703)

## 1.9.1 (November 19, 2024)

Bug fix release in the 1.9.x series.

This release adds support for Numpy 2 and Python 3.13.

> - FIX: Restore generate_gantt_chart functionality (https://github.com/nipy/nipype/pull/3290)

> - FIX: Address numpy and traits deprecations (https://github.com/nipy/nipype/pull/3699)

> - FIX: ts_Z_corr → ts_wb_Z (https://github.com/nipy/nipype/pull/3697)

> - ENH: Remove unused and recently unsupported antsRegistration flag (https://github.com/nipy/nipype/pull/3695)

> - MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3698)

## 1.9.0 (October 31, 2024)

New feature release in the 1.9.x series.

> - FIX: Remove exists=True from fsl.MotionOutliers output that might not exist (https://github.com/nipy/nipype/pull/1428)

> - FIX: Improve evaluate_connect_function errors across Python versions (https://github.com/nipy/nipype/pull/3655)

> - FIX: Changed inheritance of TensorMetricsInputSpec (https://github.com/nipy/nipype/pull/3663)

> - FIX: Add cropped files to dcm2niix output (https://github.com/nipy/nipype/pull/3609)

> - FIX: Deduplicate dcm2niix output (https://github.com/nipy/nipype/pull/3610)

> - FIX: Parse commas in CSV fields (https://github.com/nipy/nipype/pull/3637)

> - FIX: MRTrix3 change inputs position for MRTransform (https://github.com/nipy/nipype/pull/3611)

> - FIX: Use out_prefix instead of “w” in spm.Normalize12 (https://github.com/nipy/nipype/pull/3600)

> - FIX: Fix typo in spm.Normalize12 process (https://github.com/nipy/nipype/pull/3599)

> - FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596)

> - FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596)

> - FIX: Fix bugs with `fsl_out=True` and `lta_out=True` (https://github.com/nipy/nipype/pull/3583)

> - FIX: Test failures (https://github.com/nipy/nipype/pull/3587)

> - FIX: update merge_imgs input type of dcm2niix Node (https://github.com/nipy/nipype/pull/3548)

> - FIX: update sample_random_points and random_seed type of ProbTrackXBaseInputSpec (https://github.com/nipy/nipype/pull/3556)

> - FIX: update self.inputs.optimization in outputs for GTMPVC (https://github.com/nipy/nipype/pull/3571)

> - ENH: Support HDF5 (mat 7.3) SPM.mat files (https://github.com/nipy/nipype/pull/3650)

> - ENH: FILMGLS gifti output support in surface mode (https://github.com/nipy/nipype/pull/3652)

> - ENH: Added available inputs for MRTrix3’s 5ttgen (https://github.com/nipy/nipype/pull/3658)

> - ENH: Add functions to mrtrix3 interface (https://github.com/nipy/nipype/pull/3613)

> - ENH: Update PETsurfer interface (https://github.com/nipy/nipype/pull/3602)

> - ENH: Add ‘hsvs’ option to 5ttgen + mrtransform fix (https://github.com/nipy/nipype/pull/3630)

> - ENH: add STC PVC to PETPVC interface (https://github.com/nipy/nipype/pull/3634)

> - ENH: Add GenericLabel to ANTS ApplyTransforms. (https://github.com/nipy/nipype/pull/3617)

> - ENH: Issue 3553 add mvecs to dcm2niix (https://github.com/nipy/nipype/pull/3554)

> - ENH: add contrast outputs for EstimatedModel (https://github.com/nipy/nipype/pull/3577)

> - ENH: Issue 3345: Adding FreeSurfer longitudinal interfaces (https://github.com/nipy/nipype/pull/3529)

> - ENH: Enable SPM voxel-based FDR (https://github.com/nipy/nipype/pull/3558)

> - REF: Replace deprecated pkgutil.find_loader with importlib.util.find_spec (https://github.com/nipy/nipype/pull/3692)

> - REF: io.open() → open() (https://github.com/nipy/nipype/pull/3575)

> - REF: Stop using deprecated import internally (https://github.com/nipy/nipype/pull/3561)

> - DOC: Patch doc/conf.py to work with latest ReadTheDocs (https://github.com/nipy/nipype/pull/3691)

> - DOC/FIX: Fix wrong name, should be al_ea (https://github.com/nipy/nipype/pull/3629)

> - DOC: Fix typos newly found by codespell (https://github.com/nipy/nipype/pull/3606)

> - STY: Apply ruff/pycodestyle rules (E) (https://github.com/nipy/nipype/pull/3689)

> - STY: Apply ruff rules (RUF) again (https://github.com/nipy/nipype/pull/3688)

> - STY: Apply ruff/Pyflakes rules (F) (https://github.com/nipy/nipype/pull/3681)

> - STY: Apply ruff/Perflint rules (PERF) again (https://github.com/nipy/nipype/pull/3687)

> - STY: Apply ruff/flake8-comprehensions preview rules (C4) (https://github.com/nipy/nipype/pull/3686)

> - STY: Apply ruff/flake8-simplify rules (SIM) (https://github.com/nipy/nipype/pull/3676)

> - STY: Apply ruff/flake8-bugbear rules (B) (https://github.com/nipy/nipype/pull/3671)

> - STY: Apply ruff/flake8-comprehensions rules (C4) (https://github.com/nipy/nipype/pull/3680)

> - STY: Apply ruff/Perflint rules (PERF) (https://github.com/nipy/nipype/pull/3674)

> - STY: Apply ruff/flake8-implicit-str-concat rules (ISC) (https://github.com/nipy/nipype/pull/3679)

> - STY: Apply ruff/flake8-pie rules (PIE) (https://github.com/nipy/nipype/pull/3678)

> - STY: Apply ruff/flake8-raise rules (RSE) (https://github.com/nipy/nipype/pull/3677)

> - STY: Apply ruff/flynt rules (FLY) (https://github.com/nipy/nipype/pull/3675)

> - STY: Apply ruff rules (RUF) (https://github.com/nipy/nipype/pull/3673)

> - STY: Codespell (https://github.com/nipy/nipype/pull/3672)

> - STY: Apply ruff/refurb rules (https://github.com/nipy/nipype/pull/3648)

> - STY: Apply ruff/pyupgrade rules (https://github.com/nipy/nipype/pull/3647)

> - STY: Adjusted variable names for clarity and codespell false positives (https://github.com/nipy/nipype/pull/3627)

> - STY: Remove duplicated trait in EddyOutputSpec (https://github.com/nipy/nipype/pull/3568)

> - STY: Black edits (https://github.com/nipy/nipype/pull/1)

> - MNT: Replace deprecated imghdr (https://github.com/nipy/nipype/pull/3659)

> - MNT: Use regular “.now” instead of “.utcnow” with UTC zone (https://github.com/nipy/nipype/pull/3670)

> - MNT: Apply assorted repo-review rules (https://github.com/nipy/nipype/pull/3682)

> - MNT: Drop traits upper bound (https://github.com/nipy/nipype/pull/3685)

> - MNT: Configure dependabot to update GH workflows (https://github.com/nipy/nipype/pull/3597)

> - MNT: Replace deprecated locale.getdefaultlocale (https://github.com/nipy/nipype/pull/3590)

> - MNT: Require Python 3.8+, auto-upgrade syntax (https://github.com/nipy/nipype/pull/3588)

> - CI: Test Python 3.12 support (https://github.com/nipy/nipype/pull/3638)

> - CI: Test on Python 3.11 (https://github.com/nipy/nipype/pull/3589)

> - CI/FIX: configure codespell, add workflow, typos fixed (https://github.com/nipy/nipype/pull/3549)

## 1.8.6 (April 05, 2023)

Bug-fix release in the 1.8.x series.

> - FIX: Update dcmstack interface for Py3 / newer pydicom (https://github.com/nipy/nipype/pull/3541)

> - FIX: NiBabel 5, and NetworkX 3 and DIPY 1.6 compatibility (https://github.com/nipy/nipype/pull/3538)

> - FIX: Check for non-mandatory output in DWIBiasCorrect (https://github.com/nipy/nipype/pull/3523)

> - FIX: Removed leftover debug print statement in FEAT class (https://github.com/nipy/nipype/pull/3521)

> - DOC: Fix a few more typos (https://github.com/nipy/nipype/pull/3516)

> - DOC: Fix typos found by codespell (https://github.com/nipy/nipype/pull/3512)

> - CI: Drop nipy tests until a fixed nipy is released (https://github.com/nipy/nipype/pull/3559)

> - CI: Disable nipy tests generally, re-add with max numpy (https://github.com/nipy/nipype/pull/3532)

> - CI: GitHub Workflows security hardening (https://github.com/nipy/nipype/pull/3519)

> - CI: Allow tutorial test cancellation (https://github.com/nipy/nipype/pull/3514)

## 1.8.5 (September 21, 2022)

Bug-fix release in the 1.8.x series.

> - FIX: Use interpolation/method in numpy.percentile as available (https://github.com/nipy/nipype/pull/3506)

> - FIX: Deployed Matlab applications must not call addpath() (https://github.com/nipy/nipype/pull/3509)

> - FIX: Provide more runtime information when node execution fails (https://github.com/nipy/nipype/pull/3505)

> - FIX: Fixed bug for work dirs longer than 255 characters, fixes #2061 (https://github.com/nipy/nipype/pull/3495)

> - FIX: Update ApplyVDM to handle 4D inputs (https://github.com/nipy/nipype/pull/3500)

> - ENH: Explicitly specify write_text encoding format (https://github.com/nipy/nipype/pull/3508)

> - DOC: Fix typos found by copdespell (https://github.com/nipy/nipype/pull/3510)

> - MAINT: Add github action to trigger tutorials for release branches (https://github.com/nipy/nipype/pull/3504)

> - CI: Set up build-test-deploy workflow on GHA (https://github.com/nipy/nipype/pull/3513)

## 1.8.4 (September 01, 2022)

Bug-fix release in the 1.8.x series.

This release sets a maximum traits version to avoid new, breaking changes.

> - MNT: Pin traits < 6.4 (https://github.com/nipy/nipype/pull/3501)

> - ENH: Add inputs to mrtrix3.DWIPreprocInputSpec and remove mandatory annotation for pe_dir (https://github.com/nipy/nipype/pull/3470)

## 1.8.3 (July 14, 2022)

Bug-fix release in the 1.8.x series.

This release includes compatibility fixes for nibabel 4.x and resolves a denial-of-service bug when the etelemetry server is down that resulted in excessive (blocking) network hits that would cause any tools using nipype interfaces to take a very long time.

(Full changelog)

> - FIX: Argument order to `numpy.save()` (https://github.com/nipy/nipype/pull/3485)

> - FIX: Add tolerance parameter to ComputeDVARS (https://github.com/nipy/nipype/pull/3489)

> - FIX: Delay access of nibabel.trackvis until actually needed (https://github.com/nipy/nipype/pull/3488)

> - FIX: Avoid excessive etelemetry pings (https://github.com/nipy/nipype/pull/3484)

> - ENH: Added outputs’ generation to DWIBiascorrect interface (https://github.com/nipy/nipype/pull/3476)

## 1.8.2 (June 06, 2022)

Bug-fix release in the 1.8.x series.

This release restores compatibility with networkx 2.8.3, which errors when graph nodes might conflict with pydot parsing.

(Full changelog)

> - ENH: Enable compression with Gunzip interface (https://github.com/nipy/nipype/pull/3472)

> - CI: Schedule weekly tests with cron (https://github.com/nipy/nipype/pull/3480)

## 1.8.1 (May 16, 2022)

Bug-fix release in the 1.8.x series.

The previous release vendored `distutils.version.LooseVersion`, and the vendored objects did not preserve compatibility with the `distutils` objects. This release switches to the `looseversion` package that ensures compatibility.

## 1.8.0 (May 10, 2022)

New feature release in the 1.8.x series.

The primary new features are a batch of PETSurfer interfaces.

This release drops support for Python < 3.7 and Numpy < 1.17, triggering a minor version bump. Additionally, matplotlib < 2.1 will stop working with some interfaces, but more recent versions will start working.

(Full changelog)

> - FIX: Change plt.hist() argument from deprecated ‘normed’ to ‘density’ (https://github.com/nipy/nipype/pull/3455)

> - ENH: Add random seed option to ANTs registration (https://github.com/nipy/nipype/pull/3463)

> - ENH: Add PETsurfer interfaces (https://github.com/nipy/nipype/pull/3437)

> - ENH: Add Text2Vest and Vest2Text interfaces (https://github.com/nipy/nipype/pull/3447)

> - REF: Optimize ICC_rep_anova with a memoized helper function (https://github.com/nipy/nipype/pull/3454)

> - REF: Rearranging matmul order and using hermitian flag in ICC_rep_anova (https://github.com/nipy/nipype/pull/3453)

> - MNT: Drop distutils (https://github.com/nipy/nipype/pull/3458)

> - CI: Cache test data (https://github.com/nipy/nipype/pull/3459)

## 1.7.1 (April 05, 2022)

(Full changelog)

> - FIX: Allow `ConvertScalarImageToRGBInputSpec.mask_file` to be `"none"` (https://github.com/nipy/nipype/pull/3364)

> - FIX: Use a more robust strategy for detecting ANTs version (https://github.com/nipy/nipype/pull/3444)

> - FIX: Retry renaming pkl(z) files on failure (https://github.com/nipy/nipype/pull/3404)

> - FIX: Escape metacharacters when parsing dcm2niix outputs (https://github.com/nipy/nipype/pull/3417)

> - FIX: Import error for nipype.interfaces.dipy.base (https://github.com/nipy/nipype/pull/3414)

> - FIX: `ValueError` when using `ResourceMonitor` (https://github.com/nipy/nipype/pull/3419)

> - FIX: Improve error handling of `CommandLine` interfaces (https://github.com/nipy/nipype/pull/3395)

> - FIX: Bugs in ApplyVDM interface (https://github.com/nipy/nipype/pull/3396)

> - ENH: Add MRTrix3 interfaces (pared-down gh-3426) (https://github.com/nipy/nipype/pull/3445)

> - ENH: Enable BidsDataGrabber to load saved layouts (https://github.com/nipy/nipype/pull/3421)

> - ENH: ROBEX interface (https://github.com/nipy/nipype/pull/3443)

> - ENH: Include several operations to ANTs’s ImageMath interface, including ReplicateImage and ReplicateDisplacement (https://github.com/nipy/nipype/pull/3435)

> - ENH: Add “GenericLabel” to antsRegistration interpolation option. (https://github.com/nipy/nipype/pull/3424)

> - ENH: added Apply VDM functionality to FieldMap SPM interface (https://github.com/nipy/nipype/pull/3394)

> - DOC: Side bar and main page fixes (https://github.com/nipy/nipype/pull/3397)

> - TEST: Allow SVD columns to flip sign (https://github.com/nipy/nipype/pull/3405)

> - MNT: rename dipy `move_streamlines` to `transform_tracking_output` (https://github.com/nipy/nipype/pull/3412)

> - MNT: Test on Python 3.10 (https://github.com/nipy/nipype/pull/3438)

> - MNT: Added ORCID iD (https://github.com/nipy/nipype/pull/3436)

## 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 workflows (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)

## 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.