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0.5.3pre-0.6
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Changes in Nipype

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.