Changes in Nipype

Release 0.4.1 (Jun 16, 2011)

• Minor bugfixes

Release 0.4 (Jun 16, 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.