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--- neuroelf_release_notes [2011/04/30 01:59] – added features v0.9c jochen
+++ neuroelf_release_notes [2011/05/07 18:51] (current) – added v0.9c release (due to Octave compatibility) jochen
@@ Line 1: / Line 1: @@
 ====== 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) =====
@@ Line 16: / Line 26: @@
     * 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) =====