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-us...@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 ) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
