<div dir="ltr"><font face="arial, helvetica, sans-serif">Dear all,</font><div><font face="arial, helvetica, sans-serif">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.</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">For those new to Nipype, it is</font><span style="font-family:arial,helvetica,sans-serif"> 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.</span></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">More information at <a href="http://nipy.org/nipype/">http://nipy.org/nipype/</a> </font></div><div><font face="arial, helvetica, sans-serif">Installation guide at <a href="http://nipy.org/nipype/users/install.html">http://nipy.org/nipype/users/install.html</a></font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Happy holidays!</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">On behalf of all Nipype developers (</font><a href="http://goo.gl/fiyPbd" style="font-family:arial,helvetica,sans-serif">http://goo.gl/fiyPbd</a><font face="arial, helvetica, sans-serif">)</font><span style="font-family:arial,helvetica,sans-serif">,</span></div>
<div><font face="arial, helvetica, sans-serif">Chris Gorgolewski</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Changelog (since 0.8):</font></div>
<div><ul style="color:rgb(0,0,0);letter-spacing:-0.14000000059604645px;line-height:21px"><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: SelectFiles: a streamlined version of DataGrabber</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: new tools for defining workflows: JoinNode, synchronize and itersource</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: W3C PROV support with optional RDF export built into Nipype</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: Added support for Simple Linux Utility Resource Management (SLURM)</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: AFNI interfaces refactor, prefix, suffix are replaced by “flexible_%s_templates”</font></p>
</li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important"><dt><font face="arial, helvetica, sans-serif">ENH: New SPM interfaces:</font></dt><dd style="margin-top:3px;margin-bottom:10px;margin-left:30px"><ul class="" style="margin-bottom:10px;margin-top:0px!important">
<li><font face="arial, helvetica, sans-serif">spm.ResliceToReference,</font></li><li><font face="arial, helvetica, sans-serif">spm.DicomImport</font></li></ul></dd></dl></li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important">
<dt><font face="arial, helvetica, sans-serif">ENH: New AFNI interfaces:</font></dt><dd style="margin-top:3px;margin-bottom:10px;margin-left:30px"><ul class="" style="margin-bottom:10px;margin-top:0px!important"><li><font face="arial, helvetica, sans-serif">afni.AFNItoNIFTI</font></li>
<li><font face="arial, helvetica, sans-serif">afni.TCorr1D</font></li></ul></dd></dl></li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important"><dt><font face="arial, helvetica, sans-serif">ENH: Several new interfaces related to Camino were added:</font></dt>
<dd style="margin-top:3px;margin-bottom:10px;margin-left:30px"><ul class="" style="margin-bottom:10px;margin-top:0px!important"><li><font face="arial, helvetica, sans-serif">camino.SFPICOCalibData</font></li><li><font face="arial, helvetica, sans-serif">camino.Conmat</font></li>
<li><font face="arial, helvetica, sans-serif">camino.QBallMX</font></li><li><font face="arial, helvetica, sans-serif">camino.LinRecon</font></li><li><font face="arial, helvetica, sans-serif">camino.SFPeaks</font></li></ul>
<p class="" style="margin:0px 0px 0.5em"><font face="arial, helvetica, sans-serif">One outdated interface no longer part of Camino was removed: - camino.Conmap</font></p></dd></dl></li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important">
<dt><font face="arial, helvetica, sans-serif">ENH: Three new mrtrix interfaces were added:</font></dt><dd style="margin-top:3px;margin-bottom:10px;margin-left:30px"><ul class="" style="margin-bottom:10px;margin-top:0px!important">
<li><font face="arial, helvetica, sans-serif">mrtrix.GenerateDirections</font></li><li><font face="arial, helvetica, sans-serif">mrtrix.FindShPeaks</font></li><li><font face="arial, helvetica, sans-serif">mrtrix.Directions2Amplitude</font></li>
</ul></dd></dl></li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important"><dt><font face="arial, helvetica, sans-serif">ENH: New FSL interfaces:</font></dt><dd style="margin-top:3px;margin-bottom:10px;margin-left:30px">
<ul class="" style="margin-bottom:10px;margin-top:0px!important"><li><font face="arial, helvetica, sans-serif">fsl.PrepareFieldmap</font></li><li><font face="arial, helvetica, sans-serif">fsl.TOPUP</font></li><li><font face="arial, helvetica, sans-serif">fsl.ApplyTOPUP</font></li>
<li><font face="arial, helvetica, sans-serif">fsl.Eddy</font></li></ul></dd></dl></li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important"><dt><font face="arial, helvetica, sans-serif">ENH: New misc interfaces:</font></dt>
<dd style="margin-top:3px;margin-bottom:10px;margin-left:30px"><ul class="" style="margin-bottom:10px;margin-top:0px!important"><li><font face="arial, helvetica, sans-serif">FuzzyOverlap,</font></li><li><font face="arial, helvetica, sans-serif">P2PDistance</font></li>
</ul></dd></dl></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: Added simplified outputname generation for command line interfaces.</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: Allow ants use a single mask image</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important">
<font face="arial, helvetica, sans-serif">ENH: Create configuration option for parameterizing directories with hashes</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important">
<font face="arial, helvetica, sans-serif">ENH: arrange nodes by topological sort with disconnected subgraphs</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important">
<font face="arial, helvetica, sans-serif">ENH: uses the nidm iri namespace for uuids</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">ENH: remove old reporting webpage</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">API: ‘name’ is now a positional argument for Workflow, Node, and MapNode constructors</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">API: SPM now defaults to SPM8 or SPM12b job format</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important">
<font face="arial, helvetica, sans-serif">API: DataGrabber and SelectFiles use human (or natural) sort now</font></p></li><li><dl class="" style="margin-bottom:15px;margin-top:0px!important"><dt><font face="arial, helvetica, sans-serif">FIX: Several fixes related to Camino interfaces:</font></dt>
<dd style="margin-top:3px;margin-bottom:10px;margin-left:30px"><ul class="" style="margin-bottom:10px;margin-top:0px!important"><li><font face="arial, helvetica, sans-serif">ProcStreamlines would ignore many arguments silently (target, waypoint, exclusion ROIS, etc.)</font></li>
<li><font face="arial, helvetica, sans-serif">DTLUTGen would silently round the “step”, “snr” and “trace” parameters to integers</font></li><li><font face="arial, helvetica, sans-serif">PicoPDFs would not accept more than one lookup table</font></li>
<li><font face="arial, helvetica, sans-serif">PicoPDFs default pdf did not correspond to Camino default</font></li><li><font face="arial, helvetica, sans-serif">Track input model names were outdated (and would generate an error)</font></li>
<li><font face="arial, helvetica, sans-serif">Track numpds parameter could not be set for deterministic tractography</font></li><li><font face="arial, helvetica, sans-serif">FA created output files with erroneous extension</font></li>
</ul></dd></dl></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">FIX: Deals properly with 3d files in SPM Realign</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">FIX: SPM with MCR fixed</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important">
<font face="arial, helvetica, sans-serif">FIX: Cleaned up input and output spec metadata</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">FIX: example openfmri script now makes the contrast spec a hashed input</font></p>
</li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">FIX: FILMGLS compatibility with FSL 5.0.5</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important">
<font face="arial, helvetica, sans-serif">FIX: Freesurfer recon-all resume now avoids setting inputs</font></p></li><li><p class="" style="margin-right:0px;margin-bottom:0.5em;margin-left:0px;margin-top:0px!important"><font face="arial, helvetica, sans-serif">FIX: File removal from node respects file associations img/hdr/mat, BRIK/HEAD</font></p>
</li></ul></div></div>