NeuroElf wiki

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====== 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)

===== v0.9c (May 07 2011, re-release) =====
This is a re-release adding preliminary (command-line functionality only!) compatibility with [[http://www.gnu.org/software/octave/|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)

===== v0.9c (April 29 2011) =====
This is a major release with many new features.

  * added features
    * new dialog (UI) to configure the GLM computation: [[NeuroElf GUI - Compute multi-study GLM|Compute multi-study GLM]]
    * new dialog (UI) for the single-level mediation analysis: [[NeuroElf GUI - RFX mediation|RFX mediation UI]]
    * new dialog (UI) and functionality to create 3D renderings from voxel objects: [[NeuroElf GUI - Rendering UI|Rendering UI]]
    * new dialog (UI) and functionality to create VOI-based condition/trial average plots: [[NeuroElf GUI - MDM VOI condition average UI|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 [[xff - MDM format|MDM object]]: [[mdm.VOITimeCourses|MDM::VOITimeCourses]]
    * new method for common (BrainVoyager based) voxel-data objects to export as Nifti: [[aft.ExportNifti|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|AFT::SmoothData3D]]
    * new method to compute VOI-based GLM: [[mdm.ComputeVOIGLM|MDM::ComputeVOIGLM]]
    * new method to create SDMs from PRTs in an MDM object: [[mdm.SDMs|MDM::SDMs]], which is re-used in [[mdm.ComputeGLM|MDM::ComputeGLM]] and other methods
    * new function to convert [[http://wagerlab.colorado.edu/tools|Tor Wager's cluster structures]] to [[xff - VMP format|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 [[xff - PRT format|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 [[http://neuroelf.net/NeuroElf_v09c_colin_aux.zip|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|MDM::ComputeGLM]]) now supports adding subjects to an existing GLM file
    * the cluster-table method, [[vmp.ClusterTable|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 [[xff - HDR format|HDR/NII files]] (RGB and RGBA content), e.g. such as used by the [[https://www.loni.ucla.edu/Atlases/Atlas_Detail.jsp?atlas_id=15|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|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|GLM::RemoveSubject]] method now updates all ''.RunTimeVars'' subfields appropriately
    * the [[glm.SingleStudy_tMap|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|PRT::Concatenate]] method now uses the given TR correctly
    * the [[vtc.VOITimeCourse|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)

===== v0.9b (June 15 2010) =====
Mostly a service release to fix a lot of problems.

  * added features
    * added support for [[xff - ACQ format|ACQ]] (Acqknowledge) files (up to version 3.9.7, as specified in [[http://www.biopac.com/Manuals/app_pdf/app156.pdf|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
    * [[xff - SDM format|SDM]] objects created for mixed event-related design [[xff - PRT format|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|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)

===== v0.9a (May 18 2010) =====
Initial release (prior, the toolbox's functionality was available under the name [[http://support.brainvoyager.com/available-tools/52-matlab-tools-bvxqtools.html|BVQXtools]]).