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Merge pull request #1 from satra/pr1033
Pr1033
2 parents ec386ec + c750406 commit a00df37

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‎.gitignore

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.settings
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.pydevproject
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.idea/
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/documentation.zip

‎CHANGES

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* FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
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* ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
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* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
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New options also include choice of tracker, interpolator, stepsize and
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New options also include choice of tracker, interpolator, stepsize and
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curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
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* FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
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* FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
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* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
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* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
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* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
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argument formatting consistent. Cleaned ants.segmentation according to PEP8.
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(https://github.com/nipy/nipype/pull/990/files)
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* ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
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* FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
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* FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
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* ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)
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* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is
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* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is
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undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
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* FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
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* FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
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* ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
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* ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
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* ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
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Release 0.10.0 (October 10, 2014)
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============
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* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
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to enable parallel processing of very large images.
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* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
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available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
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available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
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versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
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* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
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* ENH: New dipy interfaces: Denoise, Resample
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* ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
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* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
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* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
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* ENH: New AFNI interfaces: Eval, Means, SVMTest, SVMTrain
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* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
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* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
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added to doctests, some bugs solved.
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* API: Interfaces to external packages are no longer available in the top-level
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``nipype`` namespace, and must be imported directly (e.g.
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``from nipype.interfaces import fsl``).
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* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,
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* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,
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AnalyzeWarp, PointsWarp, and EditTransform
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* ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
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* ENH: New Diffusion Toolkit interface: TrackMerge
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* ENH: New color mode for write_graph
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* ENH: You can now force MapNodes to be run serially
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* ENH: Added ANTS based openfmri workflow
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* ENH: MapNode now supports flattening of nested lists
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* ENH: MapNode now supports flattening of nested lists
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* ENH: Support for headless mode using Xvfb
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* ENH: nipype_display_crash has a debugging mode
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* FIX: MRTrix tracking algorithms were ignoring mask parameters.

‎doc/users/plugins.rst

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LSF
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---
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Submitting via LSF is almost identical to SGE above:
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Submitting via LSF is almost identical to SGE above above except for the optional arguments field:
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workflow.run(plugin='LSF')
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template: custom template file to use
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bsub_args: any other command line args to be passed to bsub.
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SLURM
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-----
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Submitting via SLURM is almost identical to SGE above except for the optional arguments field:
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workflow.run(plugin='SLURM')
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Optional arguments::
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template: custom template file to use
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sbatch_args: any other command line args to be passed to bsub.
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HTCondor
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--------
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