API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
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)
(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: 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)
replaced by https://github.com/nipy/nipype/pull/1093)
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)
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)
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)
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)
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)
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)
to enable parallel processing of very large images.
available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
ENH: New dipy interfaces: Denoise, Resample
ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
ENH: New AFNI interfaces: Eval, Means, SVMTest, SVMTrain
added to doctests, some bugs solved.
nipype namespace, and must be imported directly (e.g. from nipype.interfaces import fsl).
AnalyzeWarp, PointsWarp, and EditTransform
ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
ENH: New Diffusion Toolkit interface: TrackMerge
ENH: New MRtrix interface: FilterTracks
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()
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
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)
“flexible_%s_templates”
One outdated interface no longer part of Camino was removed: - camino.Conmap
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: 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
dipy.TensorMode
ENH: Allow control over terminal output for commandline interfaces
ENH: Added preliminary support for generating Python code from Workflows.
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
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.
ENH: Add basic support for LSF plugin.
afni.AutoTcorrelate, DcmStack
ENH: New workflows: ants template building (both using ‘ANTS’ and the new ‘antsRegistration’)
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
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
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
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
executing at any given point in time
API: crashdump_dir is now a config execution option
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
Node level)
set to True on Node level)
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
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
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
running workflows with updatehash=True option NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will rerun
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
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”
this off by specifying mandatory_inputs=False to the constructor.
API: fsl FILMGLS input “autocorr_estimate” is now called “autocorr_estimate_only”
the result directory)
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
IPython, SGE, PBS)
ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS
ENH: Optionally allows keeping only required outputs
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
and DistanceMap)
ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images
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
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 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
on all options specific to different subsampling levels
- all outputs from nodes are now pickled as part of workflow processing
- added git developer docs