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