Changes in Nipype¶
Release 0.12.0 (July 12, 2016)¶
ENH: New interface for Bruker to Nifti converter (https://github.com/nipy/nipype/pull/1523)
FIX: output file naming for FIRST outputs (https://github.com/nipy/nipype/pull/1524)
ENH: Adds fslmaths -Tstd to maths interfaces (https://github.com/nipy/nipype/pull/1518)
FIX: Selecting “gamma” in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
- ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
- ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,
https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/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 (https://github.com/nipy/nipype/pull/1201)
ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
ENH: Nipype workflow and interfaces for FreeSurfer’s recon-all (https://github.com/nipy/nipype/pull/1326)
FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
- ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
Release 0.11.0 (September 15, 2015)¶
API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
- ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)
ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)
FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)
- BUG: ANTs Registration interface failed with multi-modal inputs
(https://github.com/nipy/nipype/pull/1176) (https://github.com/nipy/nipype/issues/1175)
ENH: dipy.TrackDensityMap interface now accepts a reference image (https://github.com/nipy/nipype/pull/1091)
FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)
- ENH: Attempt to use hard links for data sink.
- FIX: Updates to SGE Plugins
- ENH: Add ants JointFusion() node with testing
- ENH: Add –float option for antsRegistration calls
- ENH: Added interface to simulate DWIs using the multi-tensor model
ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)
ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (https://github.com/nipy/nipype/pull/1136)
- FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
replaced by https://github.com/nipy/nipype/pull/1093)
- ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
- FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
fix bug in area weighted distance, and added optimizations (https://github.com/nipy/nipype/pull/1016)
ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
- ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
FIX: In the FSLXcommand _list_outputs function fixed for loop range (https://github.com/nipy/nipype/pull/1071)
ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
ENH: Added “nipype_cmd” tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
- ENH: Improve JSON interfaces: default settings when reading and consistent output creation
when writing (https://github.com/nipy/nipype/pull/1047)
FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)
FIX: Removed unused ANTS registration flag (https://github.com/nipy/nipype/pull/999)
FIX: Amend create_tbss_non_fa() workflow to match FSL’s tbss_non_fa command. (https://github.com/nipy/nipype/pull/1033)
FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)
ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)
FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)
ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/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 (https://github.com/nipy/nipype/pull/1029)
FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
FIX: Bug crashed ‘make api’ (https://github.com/nipy/nipype/pull/1026)
ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/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 (https://github.com/nipy/nipype/pull/986)
FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/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 (https://github.com/nipy/nipype/pull/1006)
FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)
- ENH: Use a while loop to wait for Xvfb (up to a max wait time “xvfb_max_wait” in config file, default 10)
Release 0.10.0 (October 10, 2014)¶
- ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
to enable parallel processing of very large images.
- ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
ENH: New dipy interfaces: Denoise, Resample
ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
ENH: New AFNI interfaces: Eval, Means, SVMTest, SVMTrain
- ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
added to doctests, some bugs solved.
- API: Interfaces to external packages are no longer available in the top-level
nipype
namespace, and must be imported directly (e.g.from nipype.interfaces import fsl
).
- ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,
AnalyzeWarp, PointsWarp, and EditTransform
ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
ENH: New Diffusion Toolkit interface: TrackMerge
ENH: New MRtrix interface: FilterTracks
- ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
are found in nipype.algorithms.metrics instead of misc. Overlap interface extended to allow files containing multiple ROIs and volume physical units.
ENH: New interface in algorithms.metrics: ErrorMap (a voxel-wise diff map).
ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()
- ENH: Deep revision of workflows for correction of dMRI artifacts. New dmri_preprocessing
example.
ENH: New data grabbing interface that works over SSH connections, SSHDataGrabber
ENH: New color mode for write_graph
ENH: You can now force MapNodes to be run serially
ENH: Added ANTS based openfmri workflow
ENH: MapNode now supports flattening of nested lists
ENH: Support for headless mode using Xvfb
ENH: nipype_display_crash has a debugging mode
FIX: MRTrix tracking algorithms were ignoring mask parameters.
FIX: FNIRT registration pathway and associated OpenFMRI example script
FIX: spm12b compatibility for Model estimate
FIX: Batch scheduler controls the number of maximum jobs properly
FIX: Update for FSL 5.0.7 which deprecated Contrast Manager
Release 0.9.2 (January 31, 2014)¶
- FIX: DataFinder was broken due to a typo
- FIX: Order of DataFinder outputs was not guaranteed, it’s human sorted now
- ENH: New interfaces: Vnifti2Image, VtoMat
Release 0.9.1 (December 25, 2013)¶
- FIX: installation issues
Release 0.9.0 (December 20, 2013)¶
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
ENH: Added support for Vagrant
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
Release 0.8.0 (May 8, 2013)¶
- ENH: New interfaces: nipy.Trim, fsl.GLM, fsl.SigLoss, spm.VBMSegment, fsl.InvWarp,
dipy.TensorMode
ENH: Allow control over terminal output for commandline interfaces
ENH: Added preliminary support for generating Python code from Workflows.
- ENH: New workflows for dMRI and fMRI pre-processing: added motion artifact correction
with rotation of the B-matrix, and susceptibility correction for EPI imaging using fieldmaps. Updated eddy_correct pipeline to support both dMRI and fMRI, and new parameters.
ENH: Minor improvements to FSL’s FUGUE and FLIRT interfaces
ENH: Added optional dilation of parcels in cmtk.Parcellate
ENH: Interpolation mode added to afni.Resample
- ENH: Function interface can accept a list of strings containing import statements
that allow external functions to run without their imports defined in the function body
ENH: Allow node configurations to override master configuration
FIX: SpecifyModel works with 3D files correctly now.
Release 0.7.0 (Dec 18, 2012)¶
ENH: Add basic support for LSF plugin.
- ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant,
afni.AutoTcorrelate, DcmStack
ENH: New workflows: ants template building (both using ‘ANTS’ and the new ‘antsRegistration’)
- ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate),
how to set SGE specific options (smri_ants_build_template_new)
ENH: added no_flatten option to Merge
ENH: added versioning option and checking to traits
ENH: added deprecation metadata to traits
ENH: Slicer interfaces were updated to version 4.1
Release 0.6.0 (Jun 30, 2012)¶
API: display variable no longer encoded as inputs in commandline interfaces
ENH: input hash not modified when environment DISPLAY is changed
ENH: support for 3d files for TSNR calculation
ENH: Preliminary support for graph submission with SGE, PBS and Soma Workflow
- ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM, MRIsSmooth,
NetworkBasedStatistic, Atropos, N4BiasFieldCorrection, ApplyTransforms, fs.MakeAverageSubject, epidewarp.fsl, WarpTimeSeriesImageMultiTransform, AVScale, mri_ms_LDA
ENH: simple interfaces for spm
FIX: CompCor component calculation was erroneous
FIX: filename generation for AFNI and PRELUDE
FIX: improved slicer module autogeneration
FIX: added missing options for BBRegsiter
FIX: functionality of remove_unnecessary_ouputs cleaned up
FIX: local hash check works with appropriate inputs
FIX: Captures all stdout from commandline programs
FIX: Afni outputs should inherit from TraitedSpec
Release 0.5.3 (Mar 23, 2012)¶
- FIX: SPM model generation when output units is in scans
Release 0.5.2 (Mar 14, 2012)¶
- API: Node now allows specifying node level configuration for SGE/PBS clusters
- API: Logging to file is disabled by default
- API: New location of log file -> .nipype/nipype.cfg
- ENH: Changing logging options via config works for distributed processing
- FIX: Unittests on debian (logging and ipython)
Release 0.5 (Mar 10, 2012)¶
API: FSL defaults to Nifti when OUTPUTTYPE environment variable not found
API: By default inputs are removed from Node working directory
API: InterfaceResult class is now versioned and stores class type not instance
API: Added FIRST interface
- API: Added max_jobs paramter to plugin_args. limits the number of jobs
executing at any given point in time
API: crashdump_dir is now a config execution option
- API: new config execution options for controlling hash checking, execution and
logging behavior when running in distributed mode.
API: Node/MapNode has new attribute that allows it to run on master thread.
API: IPython plugin now invokes IPython 0.11 or greater
API: Canned workflows are now all under a different package structure
API: SpecifyModel event_info renamed to event_files
- API: DataGrabber is always being rerun (unless overwrite is set to False on
Node level)
- API: “stop_on_first_rerun” does not stop for DataGrabber (unless overwrite is
set to True on Node level)
- API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister,
Normalize, Smooth)
ENH: Added fsl resting state workflow based on behzadi 2007 CompCorr method.
ENH: TSNR node produces mean and std-dev maps; allows polynomial detrending
ENH: IdentityNodes are removed prior to execution
ENH: Added Michael Notter’s beginner’s guide
ENH: Added engine support for status callback functions
ENH: SPM create warped node
ENH: All underlying interfaces (including python ones) are now optional
ENH: Added imperative programming option with Nodes and caching
ENH: Added debug mode to configuration
ENH: Results can be stored and loaded without traits exceptions
ENH: Added concurrent log handler for distributed writing to log file
ENH: Reporting can be turned off using config
ENH: Added stats files to FreeSurferOutput
ENH: Support for Condor through qsub emulation
- ENH: IdentityNode with iterable expansion takes place after remaining Identity
Node removal
ENH: Crashfile display script added
ENH: Added FmriRealign4d node wrapped from nipy
ENH: Added TBSS workflows and examples
ENH: Support for openfmri data processing
ENH: Package version check
FIX: Fixed spm preproc workflow to cater to multiple functional runs
FIX: Workflow outputs displays nodes with empty outputs
FIX: SUSAN workflow works without usans
FIX: SGE fixed for reading custom templates
FIX: warping in SPM realign, Dartel and interpolation parameters
FIX: Fixed voxel size parameter in freesurfer mri_convert
FIX: 4D images in spm coregister
FIX: Works around matlab tty bug
FIX: Overwriting connection raises exception
- FIX: Outputs are loaded from results and not stored in memory for during
distributed operation
FIX: SPM threshold uses SPM.mat name and improved error detection
FIX: Removing directory contents works even when a node has no outputs
FIX: DARTEL workflows will run only when SPM 8 is available
FIX: SPM Normalize estimate field fixed
FIX: hashmethod argument now used for calculating hash of old file
FIX: Modelgen now allows FSL style event files
Release 0.4.1 (Jun 16, 2011)¶
- Minor bugfixes
Release 0.4 (Jun 11, 2011)¶
- 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
Release 0.3.4 (Jan 12, 2011)¶
API: hash values for float use a string conversion up to the 10th decimal place.
API: Iterables in output path will always be generated as _var1_val1_var2_val2 pairs
ENH: Added support to nipy: GLM fit, contrast estimation and calculating mask from EPI
- ENH: Added support for manipulating surface files in Freesurfer:
- projecting volume images onto the surface
- smoothing along the surface
- transforming a surface image from one subject to another
- using tksurfer to save pictures of the surface
ENH: Added support for flash processing using FreeSurfer
ENH: Added support for flirt matrix in BBRegister
ENH: Added support for FSL convert_xfm
ENH: hashes can be updated again without rerunning all nodes.
ENH: Added multiple regression design for FSL
ENH: Added SPM based Analyze to Nifti converter
ENH: Added increased support for PyXNAT
ENH: Added support for MCR-based binary version of SPM
ENH: Added SPM node for calculating various threshold statistics
ENH: Added distance and dissimilarity measurements
BF: Diffusion toolkit gets installed
- BF: Changed FNIRT interface to accept flexible lists (rather than 4-tuples)
on all options specific to different subsampling levels
Release 0.3.3 (Sep 16, 2010)¶
- API: subject_id in ModelSpec is now deprecated
- API: spm.Threshold - does not need mask, beta, RPV anymore - takes only one image (stat_image - mind the name change) - works with SPM2 SPM.mat - returns additional map - pre topological FDR
- ENH: Added support for Diffusion toolkit
- ENH: Added support for FSL slicer and overlay
- ENH: Added support for dcm2nii
- BF: DataSink properly handles lists of lists now
- BF: DataGrabber has option for raising Exception on getting empty lists
- BF: Traits logic for ‘requires’ metadata
- BF: allows workflows to be relocatable
- BF: nested workflows with connections don’t raise connection not found error
- BF: multiple workflows with identical nodenames and iterables do not create nestsed workflows
Release 0.3.2 (Aug 03, 2010)¶
Enhancements¶
- all outputs from nodes are now pickled as part of workflow processing
- added git developer docs
Bugs fixed¶
- FreeSurfer
- Fixed bugs in SegStats doctest
Release 0.3.1 (Jul 29, 2010)¶
Bugs fixed¶
- FreeSurfer
- Fixed bugs in glmfit and concatenate
- Added group t-test to freesurfer tutorial
Release 0.3 (Jul 27, 2010)¶
Incompatible changes¶
- Complete redesign of the Interface class - heavy use of Traits.
- Changes in the engine API - added Workflow and MapNode. Compulsory name argument.
Features added¶
- General:
- Type checking of inputs and outputs using Traits from ETS.
- Support for nested workflows.
- Preliminary Slicer and AFNI support.
- New flexible DataGrabber node.
- AtlasPick and Threshold nodes.
- Preliminary support for XNAT.
- Doubled number of the tutorials.
- FSL:
- Added DTI processing nodes (note that TBSS nodes are still experimental).
- Recreated FEAT workflow.
- SPM:
- Added New Segment and many other nodes.
- Redesigned second level analysis.