[Camino-users] Nipype 0.4 release

[Chris Filo Gorgolewski]

Dear all,
I am delighted to announce release of Nipype version 0.4.

Nipype, an open-source, community-developed initiative under the
umbrella of NiPy, is a Python project that provides a uniform
interface to existing neuroimaging software and facilitates
interaction between these packages within a single workflow. Nipype
provides an environment that encourages interactive exploration of
algorithms from different packages (e.g., SPM, FSL, FreeSurfer,
Camino, AFNI, Slicer), eases the design of workflows within and
between packages, and reduces the learning curve necessary to use
different packages. Nipype is creating a collaborative platform for
neuroimaging software development in a high-level language and
addressing limitations of existing pipeline systems.

This release brings plenty of improvements. Among the most important
are: new modular executions system (direct support for PBS, SGE, and
multi-processing), support for Camino, Camino2Trackvis and Connectome
Viewer, improved parallel performance of MapNode, and growing
collection of ready to use pipelines (have a look at
nipype.workflows).

Grab it from https://github.com/nipy/nipype/tarball/0.4

For support please use our mailing list: nipy-users at googlegroups.com

Full changelog:

* 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

Enjoy!

Chris Gorgolewski on behalf of Team Nipype (
https://www.ohloh.net/p/nipype/contributors )