Changes in Nipype

Release 0.7.0 (Dec 18, 2012)

• ENH: Add basic support for LSF plugin.

• ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant,

  afni.AutoTcorrelate, DcmStack

• ENH: New workflows: ants template building (both using ‘ANTS’ and the new ‘antsRegistration’)

• ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate),

  how to set SGE specific options (smri_ants_build_template_new)

• ENH: added no_flatten option to Merge

• ENH: added versioning option and checking to traits

• ENH: added deprecation metadata to traits

• ENH: Slicer interfaces were updated to version 4.1

Release 0.6.0 (Jun 30, 2012)

• API: display variable no longer encoded as inputs in commandline interfaces

• ENH: input hash not modified when environment DISPLAY is changed

• ENH: support for 3d files for TSNR calculation

• ENH: Preliminary support for graph submission with SGE, PBS and Soma Workflow

• ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM, MRIsSmooth,

  NetworkBasedStatistic, Atropos, N4BiasFieldCorrection, ApplyTransforms, fs.MakeAverageSubject, epidewarp.fsl, WarpTimeSeriesImageMultiTransform, AVScale, mri_ms_LDA

• ENH: simple interfaces for spm

• FIX: CompCor component calculation was erroneous

• FIX: filename generation for AFNI and PRELUDE

• FIX: improved slicer module autogeneration

• FIX: added missing options for BBRegsiter

• FIX: functionality of remove_unnecessary_ouputs cleaned up

• FIX: local hash check works with appropriate inputs

• FIX: Captures all stdout from commandline programs

• FIX: Afni outputs should inherit from TraitedSpec

Release 0.5.3 (Mar 23, 2012)

• FIX: SPM model generation when output units is in scans

Release 0.5.2 (Mar 14, 2012)

• API: Node now allows specifying node level configuration for SGE/PBS clusters
• API: Logging to file is disabled by default
• API: New location of log file -> .nipype/nipype.cfg
• ENH: Changing logging options via config works for distributed processing
• FIX: Unittests on debian (logging and ipython)

Release 0.5 (Mar 10, 2012)

• API: FSL defaults to Nifti when OUTPUTTYPE environment variable not found

• API: By default inputs are removed from Node working directory

• API: InterfaceResult class is now versioned and stores class type not instance

• API: Added FIRST interface

• API: Added max_jobs paramter to plugin_args. limits the number of jobs

  executing at any given point in time

• API: crashdump_dir is now a config execution option

• API: new config execution options for controlling hash checking, execution and

  logging behavior when running in distributed mode.

• API: Node/MapNode has new attribute that allows it to run on master thread.

• API: IPython plugin now invokes IPython 0.11 or greater

• API: Canned workflows are now all under a different package structure

• API: SpecifyModel event_info renamed to event_files

• API: DataGrabber is always being rerun (unless overwrite is set to False on

  Node level)

• API: “stop_on_first_rerun” does not stop for DataGrabber (unless overwrite is

  set to True on Node level)

• API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister,

  Normalize, Smooth)

• ENH: Added fsl resting state workflow based on behzadi 2007 CompCorr method.

• ENH: TSNR node produces mean and std-dev maps; allows polynomial detrending

• ENH: IdentityNodes are removed prior to execution

• ENH: Added Michael Notter’s beginner’s guide

• ENH: Added engine support for status callback functions

• ENH: SPM create warped node

• ENH: All underlying interfaces (including python ones) are now optional

• ENH: Added imperative programming option with Nodes and caching

• ENH: Added debug mode to configuration

• ENH: Results can be stored and loaded without traits exceptions

• ENH: Added concurrent log handler for distributed writing to log file

• ENH: Reporting can be turned off using config

• ENH: Added stats files to FreeSurferOutput

• ENH: Support for Condor through qsub emulation

• ENH: IdentityNode with iterable expansion takes place after remaining Identity

  Node removal

• ENH: Crashfile display script added

• ENH: Added FmriRealign4d node wrapped from nipy

• ENH: Added TBSS workflows and examples

• ENH: Support for openfmri data processing

• ENH: Package version check

• FIX: Fixed spm preproc workflow to cater to multiple functional runs

• FIX: Workflow outputs displays nodes with empty outputs

• FIX: SUSAN workflow works without usans

• FIX: SGE fixed for reading custom templates

• FIX: warping in SPM realign, Dartel and interpolation parameters

• FIX: Fixed voxel size parameter in freesurfer mri_convert

• FIX: 4D images in spm coregister

• FIX: Works around matlab tty bug

• FIX: Overwriting connection raises exception

• FIX: Outputs are loaded from results and not stored in memory for during

  distributed operation

• FIX: SPM threshold uses SPM.mat name and improved error detection

• FIX: Removing directory contents works even when a node has no outputs

• FIX: DARTEL workflows will run only when SPM 8 is available

• FIX: SPM Normalize estimate field fixed

• FIX: hashmethod argument now used for calculating hash of old file

• FIX: Modelgen now allows FSL style event files

Release 0.4.1 (Jun 16, 2011)

• Minor bugfixes

Release 0.4 (Jun 11, 2011)

• API: Timestamp hashing does not use ctime anymore. Please update your hashes by

  running workflows with updatehash=True option NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will rerun

• API: Workflow run function no longer supports (inseries, createdirsonly).

  Functions used in connect string must be pickleable

• API: SPM EstimateContrast: ignore_derivs replaced by use_derivs

• API: All interfaces: added new config option ignore_exception

• API: SpecifModel no longer supports (concatenate_runs, output_specs). high_pass_filter

  cutoff is mandatory (even if its set to np.inf). Additional interfaces SpecifySPMModel and SpecifySparseModel support other types of data.

• API: fsl.DTIFit input “save” is now called “save_tensor”

• API: All inputs of IdentityInterfaces are mandatory by default. You can turn

  this off by specifying mandatory_inputs=False to the constructor.

• API: fsl FILMGLS input “autocorr_estimate” is now called “autocorr_estimate_only”

• API: fsl ContrastMgr now requires access to specific files (no longer accepts

  the result directory)

• API: freesurfer.GLMFit input “surf” is now a boolean with three corresponding

  inputs – subject_id, hemi, and surf_geo

• ENH: All commandline interfaces display stdout and stderr

• ENH: All interfaces raise exceptions on error with an option to suppress

• ENH: Supports a plugin interface for execution (current support for multiprocessing,

  IPython, SGE, PBS)

• ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS

• ENH: Optionally allows keeping only required outputs

• ENH: New interface: utility.Rename to change the name of files, optionally

  using python string-formatting with inputs or regular expressions matching

• ENH: New interface: freesurfer.ApplyMask (mri_mask)

• ENH: New FSL interface – SwapDimensions (fslswapdim)

• ENH: Sparse models allow regressor scaling and temporal derivatives

• ENH: Added support for the component parts of FSL’s TBSS workflow (TBSSSkeleton

  and DistanceMap)

• ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images

• ENH: Added several higher-level interfaces to the fslmaths command:

  • ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths

• ENH: added support for networx 1.4 and improved iterable expansion

• ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines

• ENH: Ability to create a hierarchical dot file

• ENH: Improved debugging information for rerunning nodes

• ENH: Added ‘stop_on_first_rerun’ option

• ENH: Added support for Camino

• ENH: Added support for Camino2Trackvis

• ENH: Added support for Connectome Viewer

• BF: dcm2nii interface handles gzipped files correctly

• BF: FNIRT generates proper outputs

• BF: fsl.DTIFit now properly collects tensor volume

• BF: updatehash now removes old result hash file

Release 0.3.4 (Jan 12, 2011)

• API: hash values for float use a string conversion up to the 10th decimal place.

• API: Iterables in output path will always be generated as _var1_val1_var2_val2 pairs

• ENH: Added support to nipy: GLM fit, contrast estimation and calculating mask from EPI

• ENH: Added support for manipulating surface files in Freesurfer:

  • projecting volume images onto the surface
  • smoothing along the surface
  • transforming a surface image from one subject to another
  • using tksurfer to save pictures of the surface

• ENH: Added support for flash processing using FreeSurfer

• ENH: Added support for flirt matrix in BBRegister

• ENH: Added support for FSL convert_xfm

• ENH: hashes can be updated again without rerunning all nodes.

• ENH: Added multiple regression design for FSL

• ENH: Added SPM based Analyze to Nifti converter

• ENH: Added increased support for PyXNAT

• ENH: Added support for MCR-based binary version of SPM

• ENH: Added SPM node for calculating various threshold statistics

• ENH: Added distance and dissimilarity measurements

• BF: Diffusion toolkit gets installed

• BF: Changed FNIRT interface to accept flexible lists (rather than 4-tuples)

  on all options specific to different subsampling levels

Release 0.3.3 (Sep 16, 2010)

• API: subject_id in ModelSpec is now deprecated
• API: spm.Threshold - does not need mask, beta, RPV anymore - takes only one image (stat_image - mind the name change) - works with SPM2 SPM.mat - returns additional map - pre topological FDR
• ENH: Added support for Diffusion toolkit
• ENH: Added support for FSL slicer and overlay
• ENH: Added support for dcm2nii
• BF: DataSink properly handles lists of lists now
• BF: DataGrabber has option for raising Exception on getting empty lists
• BF: Traits logic for ‘requires’ metadata
• BF: allows workflows to be relocatable
• BF: nested workflows with connections don’t raise connection not found error
• BF: multiple workflows with identical nodenames and iterables do not create nestsed workflows

Release 0.3.2 (Aug 03, 2010)

Enhancements

• all outputs from nodes are now pickled as part of workflow processing
• added git developer docs

Bugs fixed

• FreeSurfer
  • Fixed bugs in SegStats doctest

Release 0.3.1 (Jul 29, 2010)

Bugs fixed

• FreeSurfer
  • Fixed bugs in glmfit and concatenate
  • Added group t-test to freesurfer tutorial

Release 0.3 (Jul 27, 2010)

Incompatible changes

• Complete redesign of the Interface class - heavy use of Traits.
• Changes in the engine API - added Workflow and MapNode. Compulsory name argument.

Features added

• General:
  • Type checking of inputs and outputs using Traits from ETS.
  • Support for nested workflows.
  • Preliminary Slicer and AFNI support.
  • New flexible DataGrabber node.
  • AtlasPick and Threshold nodes.
  • Preliminary support for XNAT.
  • Doubled number of the tutorials.
• FSL:
  • Added DTI processing nodes (note that TBSS nodes are still experimental).
  • Recreated FEAT workflow.
• SPM:
  • Added New Segment and many other nodes.
  • Redesigned second level analysis.