[Mrtrix-discussion] Nipype 0.9 release

[Chris Filo Gorgolewski]

Dear all,
I am very happy to announce a new version of Nipype! Last version was
released over half a year ago and we have quite a few exciting additions.
For full list of changes see below.

For those new to Nipype, it is 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,
MRtrix, MNE, AFNI, Slicer and others), 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.

More information at http://nipy.org/nipype/
Installation guide at http://nipy.org/nipype/users/install.html

Happy holidays!

On behalf of all Nipype developers (http://goo.gl/fiyPbd),
Chris Gorgolewski

Changelog (since 0.8):

   -

   ENH: SelectFiles: a streamlined version of DataGrabber
   -

   ENH: new tools for defining workflows: JoinNode, synchronize and
   itersource
   -

   ENH: W3C PROV support with optional RDF export built into Nipype
   -

   ENH: Added support for Simple Linux Utility Resource Management (SLURM)
   -

   ENH: AFNI interfaces refactor, prefix, suffix are replaced by
   “flexible_%s_templates”
   - ENH: New SPM interfaces:
      - spm.ResliceToReference,
      - spm.DicomImport
   - ENH: New AFNI interfaces:
      - afni.AFNItoNIFTI
      - afni.TCorr1D
   - ENH: Several new interfaces related to Camino were added:
      - camino.SFPICOCalibData
      - camino.Conmat
      - camino.QBallMX
      - camino.LinRecon
      - camino.SFPeaks

   One outdated interface no longer part of Camino was removed: -
   camino.Conmap
   - ENH: Three new mrtrix interfaces were added:
      - mrtrix.GenerateDirections
      - mrtrix.FindShPeaks
      - mrtrix.Directions2Amplitude
   - ENH: New FSL interfaces:
      - fsl.PrepareFieldmap
      - fsl.TOPUP
      - fsl.ApplyTOPUP
      - fsl.Eddy
   - ENH: New misc interfaces:
      - FuzzyOverlap,
      - P2PDistance
   -

   ENH: New workflows:
   nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]
   -

   ENH: Added simplified outputname generation for command line interfaces.
   -

   ENH: Allow ants use a single mask image
   -

   ENH: Create configuration option for parameterizing directories with
   hashes
   -

   ENH: arrange nodes by topological sort with disconnected subgraphs
   -

   ENH: uses the nidm iri namespace for uuids
   -

   ENH: remove old reporting webpage
   -

   API: ‘name’ is now a positional argument for Workflow, Node, and MapNode
   constructors
   -

   API: SPM now defaults to SPM8 or SPM12b job format
   -

   API: DataGrabber and SelectFiles use human (or natural) sort now
   - FIX: Several fixes related to Camino interfaces:
      - ProcStreamlines would ignore many arguments silently (target,
      waypoint, exclusion ROIS, etc.)
      - DTLUTGen would silently round the “step”, “snr” and “trace”
      parameters to integers
      - PicoPDFs would not accept more than one lookup table
      - PicoPDFs default pdf did not correspond to Camino default
      - Track input model names were outdated (and would generate an error)
      - Track numpds parameter could not be set for deterministic
      tractography
      - FA created output files with erroneous extension
   -

   FIX: Deals properly with 3d files in SPM Realign
   -

   FIX: SPM with MCR fixed
   -

   FIX: Cleaned up input and output spec metadata
   -

   FIX: example openfmri script now makes the contrast spec a hashed input
   -

   FIX: FILMGLS compatibility with FSL 5.0.5
   -

   FIX: Freesurfer recon-all resume now avoids setting inputs
   -

   FIX: File removal from node respects file associations img/hdr/mat,
   BRIK/HEAD
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