JISCMail - SPM Archives

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One outdated interface no longer part of Camino was removed: - camino.Conmap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