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Releases: nipy/nipype

0.12.0 - Release Candidate 2

19 Jun 14:59
@satra satra
0.12.0-rc2
15a2bee
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0.12.0 - Release Candidate 2

Release 0.12.0-rc2 (June 19, 2016)

  • ENH: Adds fslmaths -Tstd to maths interfaces (#1518)
  • FIX: Selecting "gamma" in FSL Level1Design now does what the name says (#1500)
  • ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(#1493)
  • ENH: ResourceMultiProc plugin to support resource allocation (#1372)
  • ENH: Added dcm2niix interface (#1435)
  • ENH: Add nipype_crash_search command (#1422)
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (#1305)
  • FIX: job execution on systems/approaches where locale is undefined (#1401)
  • FIX: Clean up byte/unicode issues using subprocess (#1394)
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (#973)
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
    (#1090)
  • ENH: Added interfaces of AFNI (#1360,
    #1361, #1382)
  • ENH: Provides a Nipype wrapper for antsJointFusion (#1351)
  • ENH: Added support for PETPVC (#1335)
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (#1316)
  • TST: Cache APT in CircleCI (#1333)
  • ENH: Add new flags to the BRAINSABC for new features (#1322)
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (#1291)
  • FIX: Minor bugfix logging hash differences (#1298)
  • FIX: Use released Prov python library (#1279)
  • ENH: Support for Python 3 (#1221)
  • FIX: VTK version check missing when using tvtk (#1219)
  • ENH: Added an OAR scheduler plugin (#1259)
  • ENH: New ANTs interface: antsBrainExtraction (#1231)
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (#1201)
  • ENH: Interfaces for MINC tools (#1304)
  • FIX: Use realpath to determine hard link source (#1388)
  • FIX: Correct linking/copying fallback behavior (#1391)
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (#1326)
  • FIX: Permit relative path for concatenated_file input to Concatenate() (#1411)
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (#1434)
  • ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
    (#1460)
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Release candidate 1 for version 0.12.0

21 Apr 13:57
@satra satra
0.12.0-rc1
09e91c8
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Release candidate 1 for version 0.12.0

Release 0.12.0-rc1 (April 20, 2016)

  • ENH: Add nipype_crash_search command (#1422)
  • ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (#1305)
  • FIX: job execution on systems/approaches where locale is undefined (#1401)
  • FIX: Clean up byte/unicode issues using subprocess (#1394)
  • FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (#973)
  • ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
    (#1090)
  • ENH: Added interfaces of AFNI (#1360,
    #1361, #1382)
  • ENH: Provides a Nipype wrapper for antsJointFusion (#1351)
  • ENH: Added support for PETPVC (#1335)
  • ENH: Merge S3DataSink into DataSink, added AWS documentation (#1316)
  • TST: Cache APT in CircleCI (#1333)
  • ENH: Add new flags to the BRAINSABC for new features (#1322)
  • ENH: Provides a Nipype wrapper for ANTs DenoiseImage (#1291)
  • FIX: Minor bugfix logging hash differences (#1298)
  • FIX: Use released Prov python library (#1279)
  • ENH: Support for Python 3 (#1221)
  • FIX: VTK version check missing when using tvtk (#1219)
  • ENH: Added an OAR scheduler plugin (#1259)
  • ENH: New ANTs interface: antsBrainExtraction (#1231)
  • API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
  • ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (#1201)
  • ENH: Interfaces for MINC tools (#1304)
  • FIX: Use realpath to determine hard link source (#1388)
  • FIX: Correct linking/copying fallback behavior (#1391)
  • ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (#1326)
  • FIX: Permit relative path for concatenated_file input to Concatenate() (#1411)
  • ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (#1434)
Assets 2
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Release 0.11.0

15 Sep 22:07
@satra satra
0.11.0
f9c98ba
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Release 0.11.0
  • API: Change how hash values are computed (#1174)
  • ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
    (#889).
  • ENH: New interfaces for MRTrix3 (#1126)
  • ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (#1079)
  • FIX: ants.Registration composite transform outputs are no longer returned as lists (#1183)
  • BUG: ANTs Registration interface failed with multi-modal inputs
    (#1176) (#1175)
  • ENH: dipy.TrackDensityMap interface now accepts a reference image (#1091)
  • FIX: Bug in XFibres5 (#1168)
  • ENH: Attempt to use hard links for data sink.
    (#1161)
  • FIX: Updates to SGE Plugins
    (#1129)
  • ENH: Add ants JointFusion() node with testing
    (#1160)
  • ENH: Add --float option for antsRegistration calls
    (#1159)
  • ENH: Added interface to simulate DWIs using the multi-tensor model
    (#1085)
  • ENH: New interface for FSL fslcpgeom utility (#1152)
  • ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (#1136)
  • FIX: Enable absolute path definitions in DCMStack (#1089,
    replaced by #1093)
  • ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
    (#1016)
  • FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
    fix bug in area weighted distance, and added optimizations
    (#1016)
  • ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (#1002)
  • FIX: FUGUE is now properly listing outputs. (#978)
  • ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
    (#1019)
  • FIX: In the FSLXcommand _list_outputs function fixed for loop range (#1071)
  • ENH: Dropped support for now 7 years old Python 2.6 (#1069)
  • FIX: terminal_output is not mandatory anymore (#1070)
  • ENH: Added "nipype_cmd" tool for running interfaces from the command line (#795)
  • FIX: Fixed Camino output naming (#1061)
  • ENH: Add the average distance to ErrorMap (#1039)
  • ENH: Inputs with name_source can be now chained in cascade (#938)
  • ENH: Improve JSON interfaces: default settings when reading and consistent output creation
    when writing (#1047)
  • FIX: AddCSVRow problems when using infields (#1028)
  • FIX: Removed unused ANTS registration flag (#999)
  • FIX: Amend create_tbss_non_fa() workflow to match FSL's tbss_non_fa command. (#1033)
  • FIX: remove unused mandatory flag from spm normalize (#1048)
  • ENH: Update ANTSCorticalThickness interface (#1013)
  • FIX: Edge case with sparsemodels and PEP8 cleanup (#1046)
  • ENH: New io interfaces for JSON files reading/writing (#1020)
  • ENH: Enhanced openfmri script to support freesurfer linkage (#1037)
  • BUG: matplotlib is supposed to be optional (#1003)
  • FIX: Fix split_filename behaviour when path has no file component (#1035)
  • ENH: Updated FSL dtifit to include option for grad non-linearities (#1032)
  • ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
    New options also include choice of tracker, interpolator, stepsize and
    curveinterval for angle threshold (#1029)
  • FIX: Interfaces redirecting X crashed if $DISPLAY not defined (#1027)
  • FIX: Bug crashed 'make api' (#1026)
  • ENH: Updated antsIntroduction to handle RA and RI registrations (#1009)
  • ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
    argument formatting consistent. Cleaned ants.segmentation according to PEP8.
    (https://github.com/nipy/nipype/pull/990/files)
  • ENH: SPM12 Normalize interface (#986)
  • FIX: Utility interface test dir (#986)
  • FIX: IPython engine directory reset after crash (#987)
  • ENH: Resting state fMRI example with NiPy realignment and no SPM (#992)
  • FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is
    undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
  • FIX: OpenfMRI support and FSL 5.0.7 changes (#1006)
  • FIX: Output prefix in SPM Normalize with modulation (#1023)
  • ENH: Usability improvements in cluster environments (#1025)
  • ENH: ANTs JointFusion() (#1042)
  • ENH: Added csvReader() utility (#1044)
  • FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (#1083)
  • FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (#1086)
  • FIX: Add QA output for TSNR to resting workflow (#1088)
  • FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (#1096)
  • ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (#1128)
  • FIX: Fixed AFNI Copy interface to use positional inputs as required (#1131)
  • ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (#1132)
  • ENH: Use a while loop to wait for Xvfb (up to a max wait time "xvfb_max_wait" in config file, default 10)
    (#1142)
Assets 2
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