NeuroElf release notes

This page contains a per-release list of substantial additions (new features) and changes (mostly fixes) to the stable toolbox installers (or alternative flat folders)

This is a re-release adding preliminary (command-line functionality only!) compatibility with GNU Octave. Also, some minor things have changed:

• added features
  • the interpolation type can now be selected when creating montages (yielding slightly better results particularly for high oversampling factors)
• changed features
  • the cluster table output now, by default, is sorted by sign (first all clusters with positive peak value, then with negative peak value), and sub-clusters are no longer, by default, printed out with their size (to make tables more compatible with current reporting practice); both features can be changed under the extended File → Options → Clustertable sub-menu
• bug fixes
  • some smaller bugs in C-files were fixed (found during the Octave-compatibility process)

This is a major release with many new features.

• added features
  • new dialog (UI) to configure the GLM computation: Compute multi-study GLM
  • new dialog (UI) for the single-level mediation analysis: RFX mediation UI
  • new dialog (UI) and functionality to create 3D renderings from voxel objects: Rendering UI
  • new dialog (UI) and functionality to create VOI-based condition/trial average plots: MDM-VOI condition average UI
  • new screenshot functionality that allows to take high-quality screenshots of surface renderings (SHIFT + S), the GLM beta plotter, and the MDM time course plotter (both via their menu)
  • new method available to extract VOI-based timecourses from all VTC files in an MDM object: MDM::VOITimeCourses
  • new method for common (BrainVoyager based) voxel-data objects to export as Nifti: AFT::ExportNifti (this method stores the data as is with the correct transformation matrix, which allows to later re-import any subsequent result files into NeuroElf/BrainVoyager formats without quality loss)
  • new method for common voxel-based objects to smooth data: AFT::SmoothData3D
  • new method to compute VOI-based GLM: MDM::ComputeVOIGLM
  • new method to create SDMs from PRTs in an MDM object: MDM::SDMs, which is re-used in MDM::ComputeGLM and other methods
  • new function to convert Tor Wager's cluster structures to VMP objects, ac2vmp
  • new function (and datafile) to convert ICBM (segmentation-based) coordinates to TAL and back, icbm2tal and tal2icbm
  • new function to compute p/se/t-test statistics on (single-level) mediation path analysis model, mediationpset
  • new function to regress per-voxel unique models for mass-univariate cases, mmregress
  • new function to split a series of PRT files to single-trial PRTs, singletrialprts
  • new function to create icosahedron meshes, spheresrf
  • new MEX function to apply SPM normalization to coordinates (and ranges), applyspmsnc
  • new MEX function to build a vertex-based border reconstruction on a segmented voxel object, mesh_reconstruct
• added files
  • improved surface meshes and high-resolution segmentations for the colin-27 dataset (available in the NeuroElf_v09c_colin_aux.zip file; also with many derived files)
  • pre-created flatmap information to create 2D representations out of the hi-resolution reconstructed meshes
• substantially enhanced features
  • the orientation is now coded as a transformation matrix internally, so that it is fully supported for all datatypes and operations
  • painting now also works for HDR objects with any transformation matrix
  • the main menu is extended in minimized mode (adding a statistics and VOI menu to access those elements that become invisible via a menu tree)
  • the contrast manager now allows to extract VOI-based condition/contrast values per subject as covariates
  • the GLM beta plotter now also supports quadratic fit to scattered data, robust regression, legends, multi-group scattering, value scatters on bar graph overlay, subject labels on scattered values, trend lines, and confidence ellipses (for linear regressions)
  • the libSVM contribution has been updated to v3.1 (April 2011)
  • auxiliary information on objects is now stored in files with the .rtv extension instead of the .mat extension; this avoids problems when user-defined files with the same name but the .mat extension exist, and also allows information on actual .mat files to be stored
  • the GLM computation method (MDM::ComputeGLM) now supports adding subjects to an existing GLM file
  • the cluster-table method, AFT::ClusterTable, is now available for other object types (CMP, HDR, HEAD) as well
  • the NeuroElf GUI function was split into sub-functions to improve coding and debugging
  • support for compound datatypes for HDR/NII files (RGB and RGBA content), e.g. such as used by the ICBM DTI Color Atlas available at LONI)
• major bug fixes
  • colors and alpha settings are now correctly copied from displayed surface objects when undocking the window (e.g. for flat maps with statistics)
  • when deleting one of only two defined groups, now the contrast manager deletes the group definition entirely (after a request, before it would simply disable grouping, effectively disallowing to remove the definition)
  • the AFT::ReloadFromDisk method now also works for files/objects for which the filetype needs to be known (an additional parameter is passed to the call to xff when re-loading the object)
  • the GLM::RemoveSubject method now updates all .RunTimeVars subfields appropriately
  • the GLM::SingleStudy_tMap method now computes the correct .DF1 map parameter (before only the number of timepoints of the first study were used; this now allows to use this method to compute FFX contrasts)
  • the PRT::Concatenate method now uses the given TR correctly
  • the VTC::VOITimeCourse method now allows to use anatomical ROIs when using transio (before this combination likely led to an error message, given that transio access does not allow to re-use the same index more than once)
  • when using surface meshes with alphasim, the sampling now follows the configuration along the normal vector (before the sampling would always occur at vertex + 1 * normal)
  • spm5_preprojobs now correctly either removes (4D Nifti) or skips (3D Analyze volumes) the desired number of discarded acquisitions, regardless of any pre-existing data files
  • error bands are now always plotted into the correct axes when using tcplot (before, plotting into a non-current axes would plot the error bands into the currect axes object instead)
  • the xff private function dcmio now correctly reads files even if some value representation (VR) tags are incorrect
  • using the normcdfc MEX function now cannot lead to a SEGV segmentation fault (before, one value too many was processed)
  • psctrans and ztrans now correctly reject NaN/Inf values, and time-courses without variation are returned as all 0's (for ztrans)
  • when using robust regression in a N-group comparison with more than 2 groups, now all group comparisons are returned (before only the last group comparison was returned)

Mostly a service release to fix a lot of problems.

• added features
  • added support for ACQ (Acqknowledge) files (up to version 3.9.7, as specified in the documentation available at BioPac.com)
  • added the heartbeats function (and UI) to detect and manually locate heart bearts in a ECG data stream
• major bug fixes
  • SDM objects created for mixed event-related design PRTs (some conditions with durations set to 0 or 1 ms, other conditions with actual epochs) are now created correctly by using a minimal time-bin length (configurable in the options to PRT::CreateSDM)
  • creating RFX t-maps now supports the subject selection (before this information was ignored, so that contrasts would always reflect all available subjects)

Initial release (prior, the toolbox's functionality was available under the name BVQXtools).