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NeuroElf changelog

This page gives a quick overview what has changed in NeuroElf since its first publication on this website (May 17 2010) in reverse order in the following format:

  • date of change (first availability in a shapshot)
  • type of change (addition, correction, removal, etc.)
  • type of object (xff file format, xff method, function, help, etc.)
  • changed object (specific filename)
  • brief description (what exactly has changed)
  • comments (where applicable)


In case you have downloaded the very first release (or any later release for that matter), you might be interested to see if a particular feature has been added, or a problem has been worked on and solved. Coming back to this page will keep you informed about the development of NeuroElf.


Your willingness to look up this information! There is currently no email list (and I don't intend to start one; I prefer not to bother people with “updates” but for those interested, the information is of course available).

From past experiences, I suggest you check this page every other month or so for updates.


Release v0.9c (04/29/2011 through ...)

Date of change Type of change Type of object Changed Object Description Comments
11/25/2011 new function function mapestsmooth estimates smoothness of statistical map this function uses a high-resolution periodogram of 1-dimensional voxel trains to determine the underlying smoothness of a 3D image (and while the results must be used with caution and as a lower boundary!, they give a rough estimate of the underlying smoothness)
11/20/2011 new function function resestsmooth estimates smoothness of residuals (used for alphasim) this function is based on some notes about a more robust smoothness estimation, found at the FMRIB website
11/18/2011 enhancement xff method MDM::ComputeGLM this method now supports fixed-effects computations (with the RFX_GLM property set to 0) results have been compared to BrainVoyager QX's output and differences are based on the fact that Matlab's matrix inversion function (inv) produces slightly different values that BrainVoyager
11/14/2011 enhancement function fitrobustbisquare_img calls to the function can now also contain the inverse of the original covariance matrix of the design this change potentially speeds up repeated calls significantly
10/21/2011 enhancement function neuroelf_makefiles the function now also is able to produce SRF surfaces from the newly added subcortical segmentation file
10/21/2011 new file aux file colin/subcortical.nii a new file has been added that represents a 0.5mm-resolution segmentation of subcortical areas (which can be transformed into SRF surfaces using the adapted neuroelf_makefiles function)
06/13/2011 new function function recordkeys this function can be used to record key strokes with time stamps can be used alongside any other window (e.g. movie player) to record ratings
06/09/2011 enhancement function+UI ne_glmplotbetas the beta plotter now also allows to rank-transform the data for scatter plotting this was added to be compatible and consistent with maps that were created using rank-transformed contrast/covariate data
06/08/2011 enhancement function+UI fmriqasheet the window of the fMRI QA sheet now allows to manually alter the selection of to-be-discarded volumes if a valid xff object was used to create the QA sheet, the selection can also be updated in the .RunTimeVars variable for later use
06/07/2011 new feature xff method VTC::MinFrame minimizes the spatial frame of a VTC to existing data
06/07/2011 bug fix/enhancement function fdr_thresholds the default behavior fdr_thresholds is now to select the last crossing of the sorted p-values with the linearly increasing p-values before the default behavior would mimic older versions of BrainVoyager QX selecting the first (and wrong!) crossing
06/06/2011 enhancement function + UI spm5_preprojobs added the ability to create a 1mm-resolution normalized anatomical image after preprocessing this feature is not available when the data is normalized using the EPI template
06/04/2011 new feature function ne_mdmqcglobtc a new function has been added to the GUI (under Tools → Quality assessment → Create global MDM-based timecourse…) this function requests an MDM filename and then creates a time course across all runs to visualize temporal outliers (in the global time courses of runs)
06/04/2011 new feature function ne_mdmqcvtc a new function has been added to the GUI (under Tools → Quality assessment → Create averaged-volumes VTC…) this function requests an MDM filename and then creates a VTC with one (or three) volumes that represent each of the time courses so as to quickly check the spatial normalization across subjects has worked
06/03/2011 enhancement function findfiles calls with a combined path/pattern argument can now contain options, in which case the path/pattern will be correctly split
06/03/2011 enhancement xff file type PRT.tff protocols now allow to store multiple parameters per conditions this is done by setting the .ParametricWeights header field to the maximum number of parameters; conditions with less than this number of parameters must have the appropriate number of all-0 columns after the on/offsets
06/03/2011 bug fix xff file type HDR.bff saving HDR objects would not work properly for NII (one-file) objects this bug was introduced in a snapshot, so you only need to update if you are using a SNAPSHOT version!
06/02/2011 enhancement function spm5_preprojobs the VTC filename pattern in now configurable
06/02/2011 enhancement function colorpicker the colorpicker now indicates in each of the selection boxes what position is selected
06/01/2011 bug fix GUI function ne_closefile certain file types would not be correctly removed from the dropdown (e.g. anatomical/functional HEAD files)
05/31/2011 enhancement xff method PRT::CreateSDM a new parameter, diffreg, has been added, which allows to compute the difference of two regressors this can be potentially useful in cases where there are two more tonic conditions (e.g. mindsets or instructional modes) in an event-related design, which otherwise are highly colinear with the mean regressor
05/31/2011 new method xff method GLM::Anova creation of BrainVoyager compatible AVA objects this function has been moved from the _inprogress subfolder to the actual @xff/private folder, for now only the 1-within, 1-between model is implemented
05/31/2011 new function function mrmanova this function eventually will support a set of mixed-effects, repeated-measures ANOVA models for now, only the one-within/one-between factors model is implemented and tested
05/30/2011 enhancement GUI GUI menu + ne_setoption for GLM beta extraction via the GUI, the list of conditions/predictors to extract values from can now to selected via the GLM menu this allows to drop conditions of no interest (for a set of extracted values) without having to use a text editor
05/30/2011 new function function harmmean compute the harmonic mean of a numeric variable across a selected dimension
05/30/2011 enhancement GUI + xff methods GUI functions + AFT::SetColors, etc. the GUI now supports visualizing maps stored in AVA (Anova result) files
05/29/2011 enhancement xff class xff/xff as an enhancement to the xff class, syntax such as h = xff('path/pattern*.img'); will load the images (or NIftI files) matching the pattern for this syntax to work, a folder name must be given!
05/28/2011 new method xff method PLP::ClusterColorSize sets a new size and color for each point color and size depend on how many and how close points from other studies are, so that a natural clustering becomes visible (which is an informal way of looking at convergence of coordinates across studies)
05/27/2011 bug fix xff method AFT::SetScalingWindow the histogram now correctly reflects the scaled data
05/27/2011 enhancement xff class xff loading multiple headers (a cell array with *.hdr / *.img / *.nii) files is now supported and creates a HDR/NII object with all data files concatenated in the 4th dimension using the new transio feature
05/26/2011 new feature basic class transio + methods transio objects can now be created from multiple files (which must be concatenated in the last dimension) this allows to access several files (e.g. *.img files of a time series) through one variable
05/24/2011 bug fix function sdist in case the input was invalid, the 'norminv' sub-function could produce an error this was fixed, and invalid input values now properly return a NaN output
05/24/2011 enhancement function newnatresvmp the default spatial layout is now consistent with the default MNI/VTC box this change was introduced so that new VMPs are more likely to match the spatial layout of the outcome of preprocessing and regression results, e.g. for MKDA analyses
05/24/2011 renaming xff method PLP::MetaVMP → PLP::MKDA the MetaVMP method has been renamed to MKDA this was done to better represent the purpose of the method
05/24/2011 new function UI+function ne_vmp_threshmaps a new function (and menu entry under VMP → Threshold multiple maps) is available to set the threshold of multiple maps (to the same stats or p value) this function is also available in the GLM menu to threshold multiple beta maps
05/23/2011 enhancement xff method HDR::CoordinateFrame now the QFormCode != 0 algorithm for computing a transformation matrix is fully supported before, the rotation elements were ignored
05/22/2011 new method xff method SRF::ApplySPMsn apply SPM-based normalization to SRF file
05/20/2011 added feature UI+function neuroelf.tfg there are new menu entries under File → Options → Spatial normalization these entries allow to set an object-specific SPM compatible normalization file, allowing for on-the-fly normalization for visualization (without having to normalize the data on disk); also supported in Montage and Rendering functions
05/20/2011 enhancement xff methods AFT::Sample…Box + AFT::SliceData3D these methods now support the use of an optional SPM normalization parameters struct to perform full-volume and on-the-fly normalization
05/19/2011 enhancement xff method xff/subsref the DefaultProperty of the file formats now can be either a single field name or a 2-item list this allows to create more complex DefaultProperty constructs, as used in the updated PLP object (where plp.Name references the data column in plp.Points with name 'Name'
05/19/2011 new method xff method PLP::AddColumn adds a column of values to an existing PLP object if the column name already exists, the data is replaced
05/17/2011 enhancement/bug fix function + xff method ne_mdmvoicondavg + MDM::VOICondAverage this functionality would have problems with both a single value baseline window (e.g. only the onset time) as well as if only one onset per condition was given (single-trial analysis)
05/15/2011 added feature UI+function ne_loadcluster now also supports loading the files supported by VOI::ImportCluster
05/15/2011 new method xff method VOI::ImportCluster imports clusters from HDR/IMG/NII, MSK, and TXT files into an existing VOI object this allows to import images from various toolboxes as single or multiple clusters, and also creation of multiple spheres from text files
05/14/2011 new method xff method PLP::MetaVMP creates a VMP container with a set of maps (one for each study/contrast/smoothing kernel combination and a group map this is still work in progress and needs to be refined and requires a good algorithm to threshold the map
05/13/2011 added feature UI ne_setcluster when a single cluster is selected and the current slicing object has multiple volumes (4D), the average cluster timecourse is displayed in the timecourse window
05/13/2011 added feature xff method + UI AFT::SliceData3D the method now also allows to return a (2D/within-slice) gradient image on-the-fly this can be useful for instance to check the registration quality; the feature is available from the main UI via the 'g' key (or the SHIFT + 'g' combination for the underlay object)
05/13/2011 enhancement UI+function ne_cm_updateuis now the contrast manager updates other UIs (beta plotter for now) when the configuration changes before the beta plotter needed to be re-opened to reflect the changes
05/12/2011 new feature UI+function ne_markclusters clusters can now be marked as an Underlay object (of type RGB HDR) this allows to show RGB-based ROIs (comparable to BrainVoyager's functionality) on top of the actual gray-scale data; to invoke this feature, the resolution value has to be entered as a negative number, e.g. -3 for a 3mm resolution but using the new RGB overlay
05/11/2011 new feature UI+function ne_setglobaltrf the global transformation parameters (display translation, rotation, and scaling), as well as the sliced object's transformation parameters can now be set via using modifier keys and hold-dragging the mouse this works in parallel with the surface rendering transformation adaptation (SHIFT → translation, ALT → zoom, SHIFT + ALT → rotation; add CTRL for sliced object's transformation); the sliced object's transformation can be reset to the identity matrix by pressing CTRL and 'r'
05/11/2011 new method xff method AFT::VOITimeCourse the code of VTC::VOITimeCourse has been overhauled and adapted so that it now also works with (3D and) 4D Analyze/NIftI and multi-volume AFNI BRIK/HEAD files the advantage is that this allows to apply VOI coordinates directly to NII (and HEAD) objects; for compatibility reasons, the original method has been renamed to VTC::VOITimeCourseOrig
05/11/2011 enhancement transio methods transio/buffer a new functionality (buffering) has been introduced, which allows to temporarily buffer one indexing expression (e.g. one volume out of a multi-volume transio object), so that subsequent calls to, e.g. AFT::SliceToTransimg do not require to re-access the file a new ini directive/setting has been added, which for the time being is set to false but can be enabled in _core/config/xff.ini::Behavior.BufferGLMData
05/11/2011 new method transio method transio/reshape the overloading of reshape has been added
05/11/2011 enhancement function ne_clonefile this now also works for statistical objects together with the new menu entry (File → Clone stats object) this allows to use several beta plots on the same GLM data (Matlab recognizes that only one copy of the underlying data is kept in memory!)
05/10/2011 enhancement function neuroelf_setup the pre-compiled libraries (MEX files) are now available for Mac OSX 10.5 (Leopard) and 10.6 (Snow Leopard) separately the default behavior of MEX compiling is to use the most up-to-date OS SDK, which are not compatible; if the MEX files cannot be compiled, the OS version will be auto-detected and the correct libraries copied (that means that if you wish to use a shared installation for OS 10.5 and 10.6 machines, you should install on a 10.5 machine!)
05/09/2011 bug fix UI ne_setcsrfstatmap the behavior of when the Scenery and SMP list are enabled and auto-filled with objects has been improved before some UI elements could become locked (disabled) if no map was available for a surface
05/09/2011 bug fixes UI ne_glmplotbetasup the handles for text output could be plotted to the wrong axes, this has been fixed as far as I could find out, this is a Matlab bug, but a workaround has been put in place
05/09/2011 enhancement UI neuroelf_gui the height of the main UI has been reduced by about 20 pixels to better fit a regular WXVGA (WIDTH-by-768) display this also allows to use NeuroElf under 1024×768 resolution
05/07/2011 enhancement function fmriquality the quality data is automatically written into a MAT file if the input is a single object (VTC or NII file) the target filename is the source filename with extension “.fq”
05/07/2011 bug fix function writemat certain combinations of inputs would lead to incorrect files being written
05/06/2011 enhancement UI+function neuroelf_gui the way cluster tables are sorted is now configurable via the File → Options → Clustertable sub-menu
05/06/2011 enhancement method+functio clustervol.m, AFT::ClusterTable cluster table creation now supports optionally printing sub-cluster sizes (not the default) this change was introduced to make cluster tables more adhering to the community standard in publishing
04/30/2011++ compatibility functions+formats *.m, *.bff, *.tff initial compatibility with Octave (v3.4.0) was reached major changes in files: * the try, TRYBLOCK; catch eo, CATCHBLOCK; end syntax was altered (in all files using try/catch) allowing use of this construction in Octave * some residual problems were removed (e.g. characters following the continuation operator, …; stray short-circuit comparison operators were converted; where necessary, checks for whether the underlying system is Matlab or Octave were put in place; work-arounds for some minor bugs in Octave were added)

Release v0.9b (06/15/2010 through 04/28/2011)

Date of change Type of change Type of object Changed Object Description Comments
04/28/2011 enhancement UI + function ne_render_ex if the window used for rendering is closed, the procedure is canceled this is also useful to keep a certain state as the final one
04/28/2011 new function function montagemix mixes two RGB images (of same size) according to a mixing strategy replaces code prior used in ne_render_ex, ne_setsatslicepos, ne_setslicepos, and ne_vismontage_create_ex
04/28/2011 enhancement UI + function ne_mdmvoicondavgup now also supports plotting the (RFX) difference of two selected conditions (or collapsings) this can be useful to assess inferentially whether or not two conditions elicit a differential response across subjects
04/27/2011 enhancement function neuroelf_makefiles now also a “segback_hull” object is written that represents just the back-projected border of the high-resolution SRF objects this object can be used to “enclose” other content, such as the ICBM DTI atlas as RGB image, when set as an underlay
04/27/2011 enhancement UI function ne_setslicepos now supports an “underlay” object for the SliceVar object this allows to set a separate object that is rendered “below” the currently selected slice object, which can be used for enhanced drawing of ROIs or visualizing two datasets in blended mode; also supported in ne_setsatslicepos, ne_vismontage_create_ex, and ne_render_ex
04/26/2011 enhancement file format HDR.bff support for RGB and RGBA data the support is read-only at the moment! but the most important methods (AFT::SampleData3D, AFT::SliceData3D, AFT::SliceToTransimg) are supported with this datatype
04/26/2011 new method xff method HDR::InhomogeneityCorrect inhomogeneity correction for Analyze/Nifti objects mimics VMR::InhomogeneityCorrect
04/24/2011 new method xff method AFT::ExportNifti exports a BrainVoyager format (CMP/GLM/VMP/VMR/VTC/VDW) into a Nifti object this method keeps some crucial information (e.g. Maps) available for subsequent use, also integrated into the GUI
04/24/2011 enhancement UI function ne_vmp_createsmp uses the new AFT::CreateSMP a new button is available next to the list of stats maps which then only converts the current selection into SMP format
04/24/2011 new method xff method AFT::CreateSMP converted the VMP::CreateSMP method into a method valid for other objects (CMP/HDR/HEAD/GLM/VMP) gives more flexibility to what objects can be used to directly visualize on a surface mesh
04/23/2011 bug fix method @transio/size 2-output format not supported now also supports calls like
[M, N] = size(transio_object);
04/20/2011 bug fix UI function ne_cm_delgroup deleting one of the last two groups now permanently removes the group definition the user is asked whether or not he/she is certain to perform this action
04/19/2011 enhancement UI menu NeuroElf GUI added the files from the _files/colin sub-folder to the main File menu for fast access
04/18/2011 pre-release toolbox n/a v0.9c pre-release packaged, build 11041812
04/18/2011 enhancement UI + function ne_glmbetaplot ++ supports several new features among the new features are: quadratic fit to covariate, labeling of subjects in plots, trend lines, confidence ellipses, separate plot of groups (scatter), setting of scatter symbol, etc.
04/17/2011 enhancement UI function ne_clustertable the table is now printed on the console in minimized state to simplify reading cluster coordinates
04/17/2011 bug fix function heartbeats under certain conditions, the list of beats would have a number of values that led to an error message
04/16/2011 new function function neuroelf_splash this function uses a timer object to cycle through the splash images, which allows “parallel” setup and image updates
04/15/2011 bug fix xff method HDR::CoordinateFrame bug fix for the Slice1 and SliceNCenter values
04/15/2011 bug fix function colorpicker for certain values, the “reset colors” function would lead to an error the problem was introduced when the hsv2rgb function was replaced with the hsvconv MEX function
04/15/2011 enhancement UI function ne_statsmenu + ne_voimenu in minimized state, the GUI now allows access to the stats maps and VOI clusters via a main menu item
04/14/2011 enhancement xff method VMR::CleanVMR the function now uses compiled routines and is a little more robust
04/14/2011 enhancement function pmbfilter bias cutoff value and contiguity restriction added to options
04/14/2011 enhancement function dcm2nii format option added to the opts argument
04/14/2011 enhancement function singletrialprts added optional argument to force that each protocol has all (also empty) conditions this is required when the resulting SDM files are to be used with BrainVoyager QX!
04/13/2011 enhancement UI function ne_mdmvoicondavgup added support for weighted RFX (where the weight is computed by the available datapoints per subject at any given time)
04/13/2011 enhancement function + UI importrfxglmfromspms many options added to the function (incl. automatic import of VTCs, support for color settings, etc.)
04/12/2011 new function function onesamplet one-sample t-test for data where 0-values can be discarded
04/12/2011 new function function moveinlist compute new indices of items moved within a list as well as a function for re-ordering
04/12/2011 bug fix function dicom2nii spatial vectors were incorrectly set in the NII output, leading to shearing
04/10/2011 enhancement UI function ne_setcstatmapprops now also the DF1/DF2 as well as map type parameters are correctly handled same code added to ne_setcstatmapformula
04/09/2011 enhancement all M-files all M-files error handling (try/catch) now uses a caught MException object (removing a lot of LINT messages in the code)
04/07/2011 enhancement xff method SRF::Reduce now also allows to reduce irregular meshes using the preduce function of Matlab
04/06/2011 bug fix function newhdr now the correct QFormCode and SFormCode values are set in the header structure
04/04/2011 enhancement function renderlayers the M file now also contains a replacement for the MEX code, so that this function can be used prior to compiling the MEX files
04/02/2011 enhancement GUI function ne_keypress on surface-based satellite windows, the background color can now be altered using the 'b' key
04/01/2011 new function function cellipse compute coordinates for confidence-interval ellipses for bi-variate data
03/30/2011 enhancement GUI function ne_keypress keypress options have been added for satellite windows (slice and surface display in separate UIs): SHIFT+m advances the index of a displayed VMP map by one (if and only if exactly one map is selected), and SHIFT+s allows to save a screenshot (using EPS format gives high quality surface rendering options!
03/30/2011 new function GUI function ne_screenshot this function will save a screenshot of a figure or axes object of the GUI with different formats saving an axes as EPS gives high quality rendering options, e.g. in PhotoShop, etc.
03/30/2011 enhancement xff method SRF::Smooth and ::Morph the methods now allow to suppress visual output (rendering) as a speed gain (for scripted processing)
03/30/2011 enhancement function neuroelf_makefiles added back-projection VMR from hires SRF files as well as hires brain-peeled versions of colin_brain.vmr
03/30/2011 bug fix function clustervol the center-of-gravity now correctly uses the absolute value of the stats before it would use the signed value, which in case the cluster contained both negative and positive stats would be incorrectly weighting coordinates (and could even lead to NaN outcome!)
03/29/2011 bug fix xff method VTC::MeanStd the method now correctly sets thresholds as type double this now complies with the type of argument required for the thresholding functions
03/29/2011 enhancement xff method AFT::SetScalingWindow this method now also works for MSK objects the scaling window is set to 0 through 4/3 so that masked voxels are shown in light gray
03/29/2011 bug fix function spm5_preprojobs removing volumes from 4D NIftI files with repeated processing should work reliably now if data was already in the folder, the function would use the found data but then remove the volumes again
03/29/2011 new function GUI function ne_mdmvoicondavg this uses the MDM::VOICondAverage method and displays averaged time courses in its own UI extracted timecourses can be saved into a datafile for later re-load
03/28/2011 new method xff method MDM::VOICondAverage this method extracts time courses of VTCs referenced in an MDM and then computes trial-based average responses using the information found in the MDM's PRTs only works with PRT-based MDM and re-uses MDM::ConditionOnsets, MDM::SDMs, and MDM::VOITimeCourses
03/25/2011 bug fix function tcplot error bands are now always plotted into the requested axes object if the axes into which the plotting occurred wasn't the current axes (or its parent not the parent figure), error bands were plotted into a new axes
03/24/2011 enhancement xff method AFT::SliceToTransimg the method now allows to flexibly add bar graphs indicating the statistical color range to the last layer when statistical maps are rendered
03/23/2011 enhancement xff method MDM::ComputeGLM this method now re-uses MDM::SDMs this will allow future changes and added features to be used across several functions
03/23/2011 new method xff method VOI::CreateMSK this method will create a MSK object with the selected VOIs
03/22/2011 enhancement function sdist the list of statistical distributions now also comprises 'normcdf' and 'normpdf'
03/22/2011 new function function replacerobmean replace outliers (in one dimension) with robust mean estimate
03/20/2011 new method xff method DMR::Write4DNifti writes out a 4D NIftI file with DMR data
03/18/2011 enhancement xff method AFT::ClusterTable in addition to reporting the peak coordinate in the table, this now also supports reporting the center and center-of-gravity of clusters
03/18/2011 enhancement function clustervol in addition to reporting the peak coordinate in the table, this now also supports reporting the center and center-of-gravity of clusters
03/18/2011 bug fix function alphasim if a surface (SRF) was used and the along-the-normal sampling had more than one point, the sampling would always occur at vertex + 1 * normal
03/17/2011 bug fix xff method VTC::VOITimeCourse if the object is using transio, this method now correctly indexes each functional voxel only once for anatomical ROIs this method was likely to produce an error with VTCs using transio VTCData members
03/17/2011 enhancement xff method AFT::CopyObject this method now sets a handle (SourceObject) in copied objects, so that it is possible to follow back to the original
03/16/2011 new method xff method MDM::SDMs this method collects and ameliorates all SDMs from an MDM file and returns them in a cell array (either as objects or structs)
03/16/2011 new method xff method MDM::ConditionOnsets this method collects all onsets from a PRT-based MDM file and returns a cell array with the Run-by-Condition on/offset matrices
03/16/2011 enhancement xff method PRT::ConditionNames the method now also produces an option second output, the Cx3 colors of the conditions
03/16/2011 enhancement function fmriquality the detection of foreground and background voxels is now more robust (only relevant in few cases)
03/16/2011 new function function ac2vmp convert “activation_cluster” MAT files (Tor Wager tools) to BrainVoyager QX's VMP format
03/15/2011 enhancement xff method MDM::VOITimeCourses this method nows calls drawnow after extracting data from each respective VTC so as to keep the UI alive
03/14/2011 bug fix function ztrans if all values were the same, the function would return NaNs, now it returns 0's instead
03/09/2011 new function function singletrialprts conversion of a list of regular PRTs to single-trial PRTs (using PRT::ConvertToSingleTrial)
03/09/2011 enhancement xff method PRT::ConvertToSingleTrial the method now tries to create the list of condition names “in order” (across runs and subjects)
03/03/2011 bug fix GUI function ne_vismontage_create_ex images of different types can now be saved before, only JPG images could be saved due to the fix 'Quality' argument
03/02/2011 upgrade MEX functions svm files after libSVM was updated to V3, NeuroElf now has files to run SVM with V2 and V3 code
03/01/2011 bug fix private function dcmio if the value representation was invalid, the file pointer would wrongfully advance two bytes
03/01/2011 bug fix private function dicom_vr for the actual DICOM data, the “unknown” VR was incorrectly translated to 8-bit values
03/01/2011 bug fix function createfmr mosaic DICOM files were not correctly supported
02/28/2011 new method xff method FMR::Write4DNifti writes out a 4D NIftI file with FMR data
02/25/2011 bug fix GUI function ne_undock color and alpha values are now correctly copied from reference objects before, colored SRF objects produced an error when undocked
02/10/2011 enhancement function fmriqasheet an outlier detection threshold can now be optionally set
02/08/2011 bug fix xff method DMR::CoordinateFrame the coordinate frame is now correctly computed before, the origin was not correctly computed
01/27/2011 enhancement function readpar now also supports partial PAR files (i.e. in case the acquisition was stopped before the end of the run was reached)
01/26/2011 new function function reccheck fast-running basic quality check for REC (as in PAR/REC) files
12/09/2010 enhancement function vtc_concat this function required updating to reflect the newly supported (float) datatype in VTCs
12/06/2010 new function function newhdr create a new HDR/NII object with reasonable defaults
11/23/2010 bug fix xff method AFT::SetScalingWindow NaN values would lead to an error in histcount, fixed
11/23/2010 new methods xff method MTC::ApplySSM and ApplyTSM added methods to resample single-subject MTCs into group-analysis space with fixed number of vertices
11/23/2010 new function function BVQXfile/isBVQXfile added compatibility functions to re-use BVQXtools scripts
11/22/2010 enhancement function robscatter added confidence bands to regression line plot
11/21/2010 enhancement GUI neuroelf_gui the new icbm2tal is now the standard for looking up cluster peak coordinate locations both icbm2tal and tdclient checkboxes are now enabled by default
11/20/2010 new function function icbm2tal, tal2icbm conversion from and to TAL from and to ICBM space these functions use pre-computed normalization/warping parameter files derived from the Talairach.nii file using SPM8's segmentation routine, preliminary tests show a highly improved localization of structures with the TD database
11/19/2010 bug fix xff method GLM::SingleStudy_tMap while this function could be used for FFX models of any kind, it would compute the D.F. parameter incorrectly, and thus scale the statistical values improperly the bug fixed version now produces the same results as BrainVoyager QX (tested)
11/18/2010 new function function auroc area-under-ROC computation function supports vectorized input
11/05/2010 new function function reccheck perform some basic checks on a REC file (of a PAR/REC file pair) computes a mean image as well as a histogram and the peak of the bulk brain data distribution
11/02/2010 bug fix xff function tffio wrongly formatted SDM files are now (again) read correctly this bug had been fixed in the past, but was re-introduced after switching the main text-based IO to u8str2double.MEX functionality; this has been fixed by adding an additional flag to the TFF format specification, which, for SDM files, checks for this particular problem
10/27/2010 bug fix function psctrans, ztrans improper values are set to default values for instance where a voxel time course is all zero, psctrans returns all-100 values, and ztrans all-0 values
10/27/2010 new function function stoufferz implements the Stouffer-Z combination of independent z-statistics into one compound test statistic
10/25/2010 bug fix xff method SMP::Smooth the smoothing algorithm has been entirely rewritten and now results are highly comparable to BrainVoyager QX's results prior to the rewrite, the number of vertices had an undue influence, which would make smoothing of SMPs on native (non-resampled) meshes invalid
10/25/2010 enhancement GUI GLM beta plotter the beta plotter now supports group naming as well as scatter plots added to bar graphs this enriches the feature set, so that outliers can be more easily spotted when bar graphs of different groups are plotted
10/19/2010 new function function combine3danalyze combines several 3D Analyze images into one 4D NII volume
10/13/2010 enhancement function depcorrt support for robust estimation for dependent correlations was added
10/08/2010 enhancement function+GUI spm5_preprojobs support was added for different normalization methods now, also the EPI.nii template can be used, as well as session-by-session normalization (only with the EPI.template)
09/22/2010 enhancement function alphasim support was added for differentiation between one- and two-tailed statistics
09/19/2010 new UI GUI RFX mediation UI dialog to configure single-level RFX mediation based on a GLM object with configured contrasts and covariates
09/19/2010 bug fix xff method GLM::RoinRFX a check was added to assure that the same subject ID does not occur twice in the resulting GLM
09/19/2010 enhancement xff method SDM::CalcBetas the method now heeds the mtc/vtc.RunTimeVars.Discard field and automatically drops indicated time points from the model and data
09/19/2010 enhancement GUI NeuroElf main UI full support for orientation this now also includes correctly updating the crosshairs, as well as allowing the orientation to be flipped for satellite windows
09/18/2010 enhancement xff method AFT::SliceToTransimg method now supports setting the orientation (n/r) for coronal and transversal slicing
09/18/2010 enhancement GUI NeuroElf main UI closing a GLM file now closes/updates the contrast manager correctly
09/18/2010 bug fix GUI NeuroElf main UI clicking the move up/down buttons for maps on a GLM map would ask to delete the selected subject
09/18/2010 bug fix xff method GLM::RemoveSubject all fields are updated correctly now
09/18/2010 bug fix xff method MDM::ComputeGLM the filtering would only work in combination with the new PPI feature
09/17/2010 enhancement function neuroelf_makefiles now also white-matter masked (WMmasked) VMR files of the colin_brain and colin_brain_ICBMnorm files can be created
09/17/2010 enhancement GUI NeuroElf main UI the main UI now also has a brightness/contrast control bar this bar allows to set the minimal (black) and maximal (white) values for display separately for each loaded slicing object
09/17/2010 enhancement function minarray minarray now also works on logical arrays
09/17/2010 bug fix xff method GLM::RFX_tMap for robust regression between-groups, only the last comparison was returned; fixed
09/16/2010 enhancement MEX function threshlutc the function now allows more than 120 colors per tail
09/16/2010 new method xff method SRF::UpdateNeighbors neighbors that are hidden (color set to deleted) are removed so that smoothing works properly
09/15/2010 enhancement GUI contrast manager the contrast manager now allows to extract contrast covariates from currently selected contrast/VOIs
09/13/2010 enhancement xff method VMP::WriteAnalyzeVol this now fully supports the new NIftI format for SPM5/8 with the extended header
09/09/2010 enhancement function flexinterpn_method for up to 3D nearest-neighbor interpolation (without transformation) indexarray is used speed-gain factor between 8 and 12
09/08/2010 new MEX function MEX function indexarray alternative ways to access an array includes nearest-neighbor interpolation and ranges
09/04/2010 new function function mediationpset compute paths, standard errors (SE) and t stats on single-level mediation model
09/04/2010 new function function fitrobustbisquare_multi perform robust regression on multiple models
09/03/2010 new method xff method VOI::ToISO apply coordinate transformation from scanner-space to ISO-voxel-space
09/02/2010 enhancement xff method PRT::CreateSDM the PPI-feature now creates un-contrasted interactions before only contrasts could be used
09/01/2010 new method xff method AFT::SmoothData3D 3D smoothing of (partial) data allows to set spatial and value ranges
09/01/2010 enhancement MEX function conv3d now correctly discards NaN values when convolving
08/31/2010 new function function bstrapbca compute BCa boot-strap probability
08/31/2010 new function function jksample jack-knife sampling indices also creates leave-2-out samples
08/29/2010 enhancement MEX header file isinfnan.h removal of one unnecessary variable
08/29/2010 bug fix MEX function normcdfc the inner loop would process one value too many this could lead to a memory access violation
08/29/2010 enhancement function sdist added norminv to the distributions
08/28/2010 new function function bssample boot-strap sampling generator
08/28/2010 new function function mmregress multiple-model regression wrapper for pinvc and transmul functions
08/26/2010 enhancement MEX function transmul now allows to work over a 3rd dimension useful to compute regression weights and residuals of several models at once
08/25/2010 new MEX function MEX function histcount 1- and 2-dimensional histogram count with fixed bin width
08/23/2010 new MEX function MEX function pinvc multi-matrix inversion useful when several models of the same size need to be regressed
08/21/2010 new feature MAT file flatmap.mat flat maps of hires-segmentation are now provided as a convenience to display MNI-based results on a flat map maps are available in native resolution, 160k and 40k vertices resampling
08/14/2010 enhancement GUI function + tfg added VMR smoothing support to GUI smoothing allows to specify bounding box, non-integer kernel size and value range of to-be-affected voxels
08/13/2010 new function function mtimesnd N-dimensional mtimes (along higher dims) replaces the need to apply the mtimes (*) function along those dims
08/13/2010 new function function image_rotate high-quality interpolation on 2D image rotation supports gray and RGB images as well as additional options for masking
08/12/2010 new MEX function MEX function hsvconv convert from and to HSV (from/to RGB) faster than Matlab's rgb2hsv and hsv2rgb, less memory requirement
08/11/2010 bug fixes diverse diverse several smaller bugs have been fixed that could cause strange side effects with the alterations introduced earlier
08/11/2010 enhancement GUI function ne_openfile while opening a HDR file, the GUI will detect the object is the result of an SPM statistical test (e.g. t map) and will display the object as a statistical object, not an anatomical object this allows to directly load spmT_xxxx.hdr files in NeuroElf and browse maps interactively as well as creating cluster table and VOIs for later use
08/11/2010 enhancement method AFT::ClusterTable the ClusterTable method is now also available for CMP, HDR (Analyze/NIftI) and HEAD (AFNI HEAD/BRIK) objects before, these objects needed to be converted to VMPs to allow clustering
08/11/2010 enhancement function colorpicker instead of using the lazy Axes→Image overload for the CData field, the function now correctly sets the property in the image handle this reduces the number of caught errors for easier debugging and slight performance gains
08/11/2010 enhancement xff formats GLM, HDR, HEAD a new default RunTimeVars field has been added (Map) this field now stores, for each volume, the same information available in VMP objects, allowing the NeuroElf GUI to treat objects very similarly
08/11/2010 enhancement xff formats FMR, MTC, VTC a new default RunTimeVars field has been added (Discard) this will be used to keep track of volumes to be discarded during regression without the need to actually remove the data (also allowing to re-include the data at a later point in time, and also functions to enter this into the field when they detect problems)
08/11/2010 enhancement xff overloading xff/subsref+subsasgn if an object has a RunTimeVars sub-field, it can now be accessed transparently e.g. instead of writing 'obj.RunTimeVars.TrfPlus' the syntax 'obj.TrfPlus' will have the same effect
08/11/2010 enhancement xff methods AFT::… AFT methods are now only callable for those types they are meant to work on before, methods would not be listed under Help or using the TAB key, but could still be called (sometimes with strange side effects)
08/10/2010 enhancement class function xff/xff_requestfile the file requestor now retains information about the last selected file type, also a new entry (default) has been created that allows to select the more important formats directly without having to change the filter index
08/10/2010 bug fix MEX function joinlayers for certain combinations of pixel/alpha fields in layers, the code would overwrite the underlying data entirely
08/10/2010 enhancement function tffparse for expressions, the code is now only stored once
08/09/2010 new method xff method AFT::SmoothData3D allows to smooth parts of a dataset
08/08/2010 new GUI GUI + function ne_render configuration of rendering engine
08/07/2010 new GUI function GUI function ne_render_ex creation of 3D rendered brain+stats views this function works in parallel to ne_vismontage_create_ex but instead stacks the sampled images into one 3D rendered image
08/07/2010 enhancement @transimg class functions + MEX files the transimg class now also allows to store the pixel information as floating point this makes repeated calls to joinlayers (MEX function) show (almost) no rounding errors when joining several layers and returning the values several times
08/06/2010 enhancement xff method VTC::CreateGLM the VTCData is now handled in smaller packets this allows large VTCs with many beta maps to be regressed (otherwise often out of memory errors…)
08/06/2010 bug fixes functions ne_* GUI functions several smaller bugs fixed those bugs were introduced by splitting the single GUI function into several functions and did not occur before!
08/05/2010 enhancement xff method + GUI AFT::SetScalingWindow this allows to set the black-to-white scaling bounds for anatomical projects (HDR, VMR, etc.) the advantage is that, without having to re-write the data, the display can be easily adapted; still needs implementation into the GUI with new set of controls
08/05/2010 function split function neuroelf_gui GUI function split into sub-functions (in private folder) the function file (neuroelf_gui.m) had grown to over 400kB in size, which made editing slower
08/04/2010 new function function bboverlay get overlay of bounding boxes from VMR objects
08/03/2010 new function function neuroelf_makefiles this function creates derivatives of colin.img and colin.vmr files the colin.vmr file is now the only additional file created during neuroelf_setup
08/03/2010 new binary file binary file colin/seg_05mm.mat this file contains a high-resolution segmentation of the colin.vmr dataset (at 0.5mm) together with the new function, neuroelf_makefiles, this allows to create very high quality surfaces in colin-MNI and ICBM-MNI space
08/02/2010 enhancement MEX function mesh_trimapmesh an improved triangle selection is more robust (less likely to mark a vertex as non-matchable)
07/31/2010 new method xff method SRF::SetCoordsTriangles this method allows to set vertices and triangles from various sources
07/31/2010 bug fix xff method SRF::BackToVMR now the method correctly handles different resolutions and offsets
07/31/2010 enhancement xff method AFT::Browse method now also works for SMP objects
07/31/2010 amendment xff method VMR::DBReco integrating the new MEX version of the code into the xff method
07/30/2010 new MEX function MEX function mesh_neighborsarray create 2D array with neighbors (for faster computation of certain properties)
07/30/2010 new MEX function MEX function mesh_reconstruct create surface (vertices, triangles, list of neighbors) from voxel data replaces the code that was formerly part of VMR::DBReco
07/30/2010 enhancement function importvmrfromanalyze this function now supports creating VMRs in 0.5mm resolution from Analyze/NIftI files directly
07/25/2010 enhancement function + TFG neuroelf_gui several functionalities have been fixed now working: painting in altered orientation/transformed version, setting the voxel coordinate, remembering the map selection for VMP/SMPs when switching between objects, setting the threshold from the p-dropdown for surface maps
07/24/2010 enhancement function neuroelf_setup the function only creates binary files that don't already exist and also creates ICBM-PPM-atlas normalized versions of the colin dataset
07/24/2010 new MEX function MEX function applyspmsnc apply SPM's _sn.mat normalization to coordinates (both ways) used in the new setup that creates ICBM-normalized colin_*.* files
07/24/2010 enhancement MEX header quattrans.h now has a second set of variables/functions this is useful in cases where a function has two separate quaternions for multiplication
07/23/2010 enhancement xff method SRF::BackToVMR the back-projection now samples throughout the triangles this leads to a much denser representation of the surface (with configuration “depth”)
07/21/2010 enhancement function neuroelf_setup the function only creates binary files that don't already exist and also imports a VMR from the now bundled Analyze version of the colin dataset this dataset can be downloaded from the CBU Imaging wiki
07/21/2010 added file binary file colin/colin.hdr+img I decided to bundle the hdr/img instead of the VMR the VMR file will be created and masked during neuroelf_setup; while this file is slightly larger after compression, it still has the full intensity range, which might improve segmentations, etc.
07/20/2010 altered file binary file colin/sph.mat coordinates for LH and RH are now in new notation (for own function) this allowed to drop the sph80.mat file in the srf folder (coming from BrainVoyager), also coordinates are now saved as uint16 (BV-voxel position * 256), which saves some more space
07/20/2010 re-implementation function spheresrf create a icosahedron sphere mesh results will differ from BrainVoyager w.r.t. vertex numbering and triangle order!!
07/20/2010 new function function dividetrimesh divide triangles in a mesh splits each side of the triangle, thus quadrupling the number of triangles (and almost vertices)
07/12/2010 new function function flexplot flexible plotting ALPHA stage
07/09/2010 enhancement xff method MDM::ComputeGLM the function now reads a pre-existing GLM and updates/add subjects as requested this allows to re-run an RFX-MDM with new subjects without the need to re-run all subjects, especially useful for robust regression!
07/08/2010 new function function vtcregressout convenience function that reads multiple RTC/SDM files and saves the resulting VTC
07/08/2010 new method xff method VTC::RegressOut regressing out of nuisance regressors from a VTC
07/08/2010 new method xff method VTC::MeanSRFTimeCourse extract the mean time course of a surface from a VTC this is usefule e.g. for regressing out a global gray-matter time course
07/07/2010 bug fix function spm5_preprojobs skipping with 4D NII files now does the right thing! before, volumes were removed but then, the same number of volumes was additionally skipped…
07/07/2010 enhancement function showspmrparams the default colors are now as in SPM's display
07/06/2010 new method xff method AFT::Info getting additional information on objects (for now only PRT, but will be extended) this is useful for regularly occurring tasks, such as getting an idea of the distribution of onsets in a PRT across conditions, etc.
07/06/2010 enhancement xff method SDM::AddFilters now supports to add filters only to “part of” an SDM (in time) useful when the underlying PRT represents several sessions (e.g. after concatenation; potentially better for robust regression on the first level to have an improved initial regression outcome which then determines the outliers!)
07/06/2010 enhancement xff method MDM::ComputeGLM the method now supports orthogonalization of the nuisance regressors (also with the filter) same option added also to MDM::ComputeVOIGLM
07/06/2010 bug fix xff method PRT::Concatenate the TR was not correctly taken into account the bug was relevant when the resolution of time was set to msec
07/05/2010 GUI dialog function function + TFG neuroelf_gui a first working version of the MDM → GLM computation has been added currently this is only without options → next snapshot!
07/05/2010 enhancement xff method MDM::ComputeGLM now also the derivatives of the motion parameters can be added to the model (as confounds)
07/05/2010 enhancement function findfiles the use of '?' as single-character wildcard is now supported MATLAB's internal dir function does not support the '?' wildcard on all (any?) systems, this is now supported
07/05/2010 bug fix function rbalign if the second argument wasn't double, an error occurred fixed
07/05/2010 new method xff method MDM::ComputeVOIGLM perform GLM regression (OLS or robust) on time courses extracted from VOIs internally calls mdm.VOITimeCourses
07/05/2010 new method xff method GLM::GenerateMDM for a given RFX GLM file/object, an MDM can now be (re-) generated useful to re-run a model without having the MDM file at hand
07/05/2010 bug fix xff format GLM.bff when only the header was to be loaded, a syntax error would occur fixed
07/05/2010 bug fix xff format HDR.bff better support for Analyze DataTypes datatypes for uint16 and uint32 were only supported for the old enumerator, now the new values (512, 768) are supported
07/05/2010 new method xff method VTC::Write4DNifti saves the content of a VTC as a four-dimensional NIftI file
07/05/2010 new method xff method MDM::VOITimeCourses extract time courses of VOIs from all linked VTCs of an MDM
07/04/2010 new method xff method MDM::Subjects returns the subject IDs of functional files in an MDM the list is either unique (in the order of first subject appearance) or represents the ID of the functional file (via argument to the method)
06/29/2010 enhancement xff method GLM::RFX_rMap better automatic naming of maps; allows to add several covariates into one model
06/28/2010 new methods xff method MAT::* added NTT object methods to MAT object (for compatibility)
06/28/2010 new figure tfg object neuroelf_physio.tfg GUI-based configuration of physio data processing very early stage
06/28/2010 enhancement function heartbeats error handling has been improved and additional pre-calculations have been added
06/28/2010 enhancement function fmriqasheet added a second parameter to set the outlier detection threshold from the different criteria
06/25/2010 enhancement xff method MDM::ComputeGLM mdm.ComputeGLM now passes all options transparently to PRT::CreateSDM (e.g. HRF shape, etc.)
06/24/2010 filename change xff aux file obj.matobj.rtv the file storing the RunTimeVars content has been renamed to XFF_OBJECT.rtv this was done to cope with the fact that MAT files can now be loaded and saved as xff objects
06/24/2010 new xff format xff format MAT.bff load MAT files into an xff object some minor changes in bffio.m and xff.m have been made to cope with this new format
06/24/2010 new function function writemat.m write a MAT file with specific variable names/content
06/24/2010 new function function fieldsize.m returns the size (in bytes) of one or several fields of a struct
06/24/2010 name correction xff format MAP.bff renamed NameOfSSMFile to NameOfSDMFile the field name for the design matrix file was wrongly named
06/24/2010 bug fix xff format PRT.tff when FileVersion was set to 3 and ParametricWeights to 0, conditions were not read at all while this is compliant with BrainVoyager's way to write PRT files, it doesn't make sense to prohibit this combination of values
06/23/2010 enhancement xff method MAP::CreateVMP now, also lanczos3 is supported as interpolation (for really high-quality/no-smoothing interpolation)
06/23/2010 bug fix function spmshowrparams when trying to read from 3D volumes in multiple runs the function would produce an error fixed some internal counting variable (being set to 0 incorrectly between runs
06/22/2010 bug fix xff method VMR::ApplyTRF the difference in coordinate system origin was not taken into account see vmrspmcoreg, the fixed version was tested against BrainVoyager QX v2.1.2 yielding identical results using lanczos3 interpolation method when compared to BV's sinc interpolation
06/22/2010 bug fix function vmrspmcoreg the difference in coordinate system origin was not taken into account BrainVoyager applies rotations (in VMR space) around TAL coordinate [0.5, 0.5, 0.5] (to account for the fact that datasets usually have even-numbered dimensions, e.g. 256-by-256-by-256 for VMRs)
06/21/2010 bug fix function custom_pwelch corrected a bug that could lead to missing a window when sliding
06/20/2010 added option xff method ACQ/NTT::SampleData another input argument, ui, was added to specify a method of up-sampling interpolation instead of the default (cubic spline), the user can now also use linear and nearest neighbor interpolation for display
06/20/2010 enhancement MEX file flexinterpn.c added support for variable kernel windows per dimension this allows both a 4D data block to be smoothed in only three of four dimension and also to correctly apply a temporal filtering kernel in only one of several data dimensions
06/20/2010 feature request function plotcurves added support for “find peak-in-window keyboard shortcut”
06/20/2010 enhancement function resampleaa altered the cubic+smoothing window to be of proper width, adaptive gaussian window size larger gaussian windows are now no longer resampled to 4096 samples per kernel bin, which allows to downsample a large set of data (e.g. 20 minutes of recording) for display in very little time
06/19/2010 enhancement function prefilter added post-filtering step and improved argument syntax all lengths, etc. are now given in the time domain (not in samples)
06/19/2010 overhaul rework function + TFG plotcurves added features: zooming, spot moving, variable access, filtering, etc. major work on this function; please update to SNAPSHOT if you need it!
06/18/2010 potential bug fix MEX file flexinterpn.c the kernelsize was restricted to 127 (datatype signed char) while this is enough for any standard interpolation, when the function is used to smooth/resample with large kernel sizes > 127 elements, it would return zeros; the datatype used now is signed short allowing kernel sizes of up to 32767 (should be enough for any resampling scale!)
06/18/2010 new method xff method NTT:Resample mimicking ACQ::Resample
06/18/2010 new method xff method NTT:Filter mimicking ACQ::Filter
06/18/2010 new method xff method NTT:ChannelData mimicking ACQ::ChannelData
06/18/2010 bug fix xff method AFT:ReloadFromDisk for objects that need their file format known (generic extension), the file format (primary extension) is now passed to xff on reload this fixes the problem with reloading generic NTT (and some other) data files
06/17/2010 figure improvements tfg figure plotcurves.tfg resizing dialog, adding variable labels/edit fields and overview axes object
06/17/2010 new method xff method ACQ::Filter passing ACQ channel data over to prefilter
06/17/2010 new method xff method ACQ::Resample passing ACQ data over to resampleaa
06/17/2010 new method xff method ACQ::ChannelData returns channel data from either Channel(C).Data or RawData(C, :) correctly takes Scaling into account; stores Result in Channel(C).Data if necessary
06/17/2010 new function function prefilter pre-filters a physiological measurement channel/data using the first and second discreet derivative to find spiky areas and remove those
06/17/2010 new function function resampleaa resampling with anti-aliasing filter uses flexinterpn_method, flexinterpn and smoothkern
06/17/2010 bug fix function fmriquality if no progress bar object was created, the motion detection would produce an error the error is caused by a missing variable from an if/else/end statement earlier
06/17/2010 enhancement function fmriqasheet the output of the non-motion-parameters call/struct has been improved to use the entire figure space
06/17/2010 bug fix function acsvread now over-long rows don't produce an error for struct output
06/16/2010 renaming function windsorize → winsorize corrected the name of the function to conform with the actual procedure name the person whom this is named after is Charles P. Winsor
06/16/2010 help/feature correction xff method PRT::CreateSDM the PRT::CreateSDM method showed optional parameters .regi and .regni in the help, but those were never actually processed while adding regressors of (no) interest to an existing SDM is simple, it might yet be good to have this option working for scripting purposes; bug/missing feature found by Fraser Smith
06/15/2010 bug fix xff method GLM::RemoveSubject group subject indices are now correctly patched prior to the bug, the subject indices in the configured groups in .RunTimeVars were not updated correctly

Release v0.9a (05/17/2010 through 06/15/2010)

Date of change Type of change Type of object Changed Object Description Comments
06/15/2010 enhancement function neuroelf_gui improvement to accept column names for covariates in a .mat files a covariate .mat file can now contain two variables, a table and a list of column names (cell array)
06/15/2010 bug fix xff method GLM::RFX_rMap the function now correctly accepts a subject selection from the contrast manager UI
06/14/2010 enhancement function heartbeats added two more options, plotfreq and skewdt allowing to set the samples/second for the final plot and also the factor to compute the detection threshold from the skew value
06/11/2010 new MEX function C source + MEX normcdfc normal cumulative distribution function
06/11/2010 bug fix function spmmat2sdm multiple sessions are now correctly supported in case of multiple sessions (very often the case), the row and column indices from which the SDMMatrix was extracted from the xX.X field in the SPM.mat structure were wrong; this has been fixed. Additionally, the names of multiple sessions now correctly uses an underscore instead of a hyphen character to separate subject ID from session number (this has also been changed in spmmat2prt for having equal output names)
06/10/2010 renaming function bfastica → ne_fastica the function bfastica was renamed to ne_fastica this change was done to reflect the toolbox name
06/10/2010 bug fix xff method GLM::RFX_tMap the subsel field (which was used by the neuroelf_gui) was not supported by this method; this is now fixed
06/10/2010 bug fix xff method PRT::CreateSDM added full support for real event-related designs (stimulus length = 0) prior to this, such events were discarded instead of modeled; for those events, a default length (default value 100ms) can be given as a new option
05/31/2010 new GUI feature function neuroelf_gui added the requested “echo mode” (important calls to functions and methods are printed in the Matlab prompt as templates for creating scripts per request of Nick Ketz
05/31/2010 new GUI menu item figure + code neuroelf_gui added a menu item that requests user options and then calls vmp.CreateMSK if the currently selected stats object is a VMP with at least one selected map per request of Ethan Kross
05/31/2010 new method xff method VMP::CreateMSK ability to create a BrainVoyager QX compatible MSK object from a (sub-) selection of maps in a VMP per request of Ethan Kross
05/30/2010 extension class method @?/any2ascii any2ascii support added for transimg, xff, and xfigure this allows to use the general any2ascii routine with variables (structs) that have one of those object types embedded
05/30/2010 enhancement function tffio implementation of u8str2double into tffio reading of large text tables (SDM, FBR) should be much faster, given that tffio now uses u8str2double instead of eval
05/30/2010 extension c source + MEX u8str2double the function now accepts two additional parameters (both must be given or none), number of rows and number of columns, which also skips the first pass to detect the number of both; in this case, the function also returns how many characters remain at the end of input stream; also the function now supports input of char arrays changes made for compatibility with tff input and eval, slight decrease in speed (more checks, etc.) but still faster than eval for larger tables
05/28/2010 new file format binary format NTT.bff this format is used to read in large text-based files uses the new u8str2double MEX function, supports variable header lines (up to 16384 bytes) at the beginning of file, information stored in .Header struct; necessary addition to xff.m: format can be forced for files with generic extension as second argument: obj = xff(filename, format);
05/28/2010 new MEX function c source + MEX u8str2double this function parses a large text-based table (stored in a uint8 variable!) about 8 times faster than Matlab's internal function (used by textread), support for “short rows” (values set to NaN), useful if last row is incomplete
05/28/2010 GUI layout figure + code heartbeats_cleanup.tfg the UI for the cleanup of heartbeats now has several additional features: buttons for previous window, remove all feature (for noisy data), small overview time-course plot with noise estimate and quick-jump function
05/28/2010 bug fix method VTC::ICA prior to the fix, the number of MapParameters was incorrectly set to the number of components
05/27/2010 bug fix function tcplot corrected the use of one of Matlab's internal graphics handle settings
05/27/2010 new function function heartbeats detect the heartbeats (and heart-rate) from an ECG channel data stream includes own UI to manually correct flaws
05/25/2010 new feature method VTC::CrossCorrelate now supports the .lag flag in options, useful when the auto-correlation of a VTC is to be computed simply use a call such as vmp = vtc.CrossCorrelate(vtc, struct('lag', 1));
05/24/2010 new file format binary format NLF.bff NeuroElf's own file format to store a variety of objects (voxel data, surfaces, stats, experimental design, etc.) this is still very preliminary and not yet functional! already applied changes to AFT::BoundingBox, aft::ConvertToNLF, AFT::GetVolume, AFT::GetVolumeSize, AFT::IntensityMask, AFT::SampleBVBox, AFT::SampleData3D, AFT::SampleTalBox, AFT::SetOrientation, AFT::SliceData3D, AFT::SliceToTransimg; also added NLF::CoordinateFrame
05/24/2010 new function function showspmrparams visualizes the realignment parameters as detected by SPM's preprocessing reads either the quaternion transformations from the volumes that were motion-estimated (usually aVOLUMENAME.hdr/nii), but also supports using the information from the rp_VOLUME.txt files (which does not contain the motion between but only across runs, however!)
05/24/2010 internal rename function neuroelf_gui internally renamed all functions from bt_NAME to ne_NAME simply for consistency
05/22/2010 new function function vmrspmcoreg create a BrainVoyager-compatible TRF file to apply the coregistration transformation between two VMRs per request of Jan Willem Koten and Hannes Schwenke, new file: _files/spm/spm5_coreg.mat
05/21/2010 new feature method SRF::AddMarkers the method now also supports unit-cubes as shapes new file: _files/srf/unitcube.srf
05/21/2010 extension function smoothkern limitation for kernel sizes increased necessary to generate larger 1-D kernels
05/21/2010 new file format binary format ACQ.bff added support for ACQ (Acqknowledge) files up to version 3.9.7 documentation used available from
05/21/2010 bug fix method PLP::PlotOnSurface better support for user-specified SRF objects before, the provided colin_LH and colin_RH objects were still displayed
05/21/2010 bug fix method PLP::PlotOnSlice corrected the lookup of axes object and children was necessary after switching the default in xfigure to hide children from findobj
05/20/2010 new feature class function @transio/any2ascii any2ascii is overloaded for transio, so that objects can be stored in ASCII representation
05/20/2010 new method method XFF::ClearObjects the xff (root) object can now clear objects specified by a filename pattern
05/20/2010 GUI feature figure code neuroelf_gui button and code added that allows to jump to the nearest peak (first) voxel the list of voxels to consider is taken from the list of VOIs, not the current statistical map!
05/20/2010 GUI layout button icon trash.tif added a red X to the trashcan icon suggestion by Hedy Kober to make the icon more distinguishable
05/20/2010 GUI layout figure neuroelfbasic.tfg added the split local maxima option as checkbox to the GUI change required layout rearrangement
05/20/2010 feature addition function findfirst added the non-MEX code, so that findfirst works (even if slower) also when the compiled file does not exist
05/20/2010 bug fix function renamefile changed the internally used mechanism to rename files (for Windows) on Windows 7 machines, the usage of the shell based rename command is problematic (only works if the folder is not overloaded in a user's virtual storage
05/18/2010 bug fix function tempfilter nuisance regressors are now better checked for validity (before it could happen that badly prepared nuisance regressors would invalidate the filtering)
05/18/2010 new method method SDM::ShowDesign SDM::ShowDesign visualizes the design matrix of a single session in one of three ways: a) gray scale image (with time running from top to bottom and regressors from left to right; brighter spots being higher values; this is the SPM-typical way to show a design matrix), b) orthogonality information (demonstrating the high-dimensional angle between regressor (white: completely orthogonal, black: completely collinear), c) as time-course plots (time running from left to right; regressors ordered top to bottom; incl. a legend) added option to MDM::ComputeGLM to show each design matrix while the GLM is computed
05/17/2010 feature addition function flexinterpn_method added the capability to apply a rotation to a two-dimensional matrix (before only possible with 3D data), the rotation parameters must still be working on the 2nd and 3rd dimension; internally, the input will simply be dim-shifted
05/17/2010 feature addition function initialalignment added the capability to work on two VMRs (instead of VMR and FMR), allowing to run the function to estimate the initial alignment (IA) file between two VMRs
neuroelf_changelog.1322256548.txt.gz · Last modified: 2011/11/25 22:29 by jochen