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| neuroelf_changelog [2014/06/01 13:10] – added until 1/13/2012 jochen | neuroelf_changelog [2014/06/09 02:12] – added 06/08/2014 jochen |
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| ===== Changelog ===== | ===== Changelog ===== |
| |
| ==== Release v0.9c (04/29/2011 through ...) ==== | ==== Release v0.9d (03/13/2014 through ...) ==== |
| ^ Date of change ^ Type of change ^ Changed Object ^ Description ^ Comments ^ | ^ Date of change ^ Type of change ^ Changed Object ^ Description ^ Comments ^ |
| | | 06/08/2014 | new GUI feature | neuroelf_gui | the main GUI now supports resizing (larger), and the size at closing time is stored, such that the GUI opens in the same configuration as before | | |
| | | 06/08/2014 | enhancement (GUI) | ne_swapfullsize.m | the swapping of full and reduced sizes is much faster now | | |
| | | 06/08/2014 | new GUI feature | ne_draw_histmarked.m | a histogram of marked voxels can be displayed to estimate the peaks for gray and white matter | | |
| | | 06/07/2014 | enhancement | ne_undock.m | when undocking a slicing or rendering satellite, the global field ''ne_gcfg.tio.satSag'' or ''ne_gcfg.tio.satRnd'' will be set | | |
| | | 06/07/2014 | bug fix (xff code) | AFT::RenderToTransimg | the negative tail could have its maximum cut off (invisible) | | |
| | | 06/07/2014 | enhancement | all UIs/figures | now the HandleVisibility is set to '''callback''' on all figures to prevent accidental drawings inside them | | |
| | | 06/06/2014 | bug fix (GUI) | ne_btdown.m, ne_btmove.m | drawing is now prevented when clicking somewhere within the GUI that is not directly on top of the slice displays | | |
| | | 06/06/2014 | enhancement | @xff/subsasgn.m | removed necessity to create a copy of large fields in the contents of xff objects by using a more direct sub-field assignment operation | this only increases performance if the field is on the first level of fields, such as ''vmr.VMRData'' | |
| | | 06/06/2014 | new GUI feature | neuroelf_gui.tfg | some default choices have been added to set the color lookup table for grayscale objects | | |
| | | 06/06/2014 | enhancement | AFT::SliceData3D | major speed improvement when using regular (full-space, integer-coordinate) sampling for HDR (NII) objects | | |
| | | 06/06/2014 | enhancement (MEX) | indexarraynb.c | now the coordinate range-syntax also supports four-dimensional arrays | | |
| | | 06/06/2014 | enhancement | AFT::RenderToTransimg, ne_setslicepos.m | now also the VMRData16 component of VMR objects can be rendered and displayed in the GUI directly | | |
| | | 06/05/2014 | enhancement (GUI) | ne_setslicepos.m, ne_draw.m | code has been moved into a new file and substantially expanded and cleaned, which now allows to fix-color as well as multiply-color areas | | |
| | | 06/04/2014 | enhancement | AFT::GetVolume, AFT::SampleBVBox, AFT::SampleTalBox | added support to retrieve alpha volume from objects that support them (e.g. Average-timecourse VTCs) | | |
| | | 06/02/2014 | bug fix (MEX) | cov_nd.c | for lag 0, the function was supposed to run the covariance/correlation along the first dimension | | |
| | | 05/29/2014 | enhancement | ne_glmplotbetasup.m | when updating the beta plotter, a faster access for non-normalized data (based on template space coordinates) has been implemented | | |
| | | 05/28/2014 | enhancement | AFT::MapNames | additional information about maps (type, D.F.) can be requested with an extended flag | | |
| | | 05/22/2014 | new GUI feature | neuroelf_gui | a tool to average structural/anatomical datasets has been added, supporting spatial normalization and brain extraction | | |
| | | 05/21/2014 | enhancement | MDM::ComputeGLM, SDM::CalcBetas | instead of storing beta maps, single-regressor t-maps can now be computed to facilitate later RSA (representational similarity analysis) application | | |
| | | 05/05/2014 | enhancement (GUI) | ne_cm_compute.m, GLM::RFX_tMap | contrast maps (weighted sums of beta maps) can now be smoothed "late" (immediately prior to computing random-effects statistics) | | |
| | | 05/04/2014 | enhancement (GUI) | spm5_preprojobs | an option has been added to import VTCs after realignment (using non-normalized, unsmoothed data for GLMs) | | |
| | | 05/03/2014 | enhancement | AFT::GetVolume, GLM::VOIBetas, MDM::ComputeGLM | RFX-GLM files can now contain non-normalized data alongside the normalization information (read, for instance, from the STRUCT_seg_sn.mat file) | | |
| | | 05/01/2014 | enhancement | importvtcfromanalyze | subject-space data can be imported and the SPM-based normalization parameters stored in the RunTimeVars property | | |
| | | 04/17/2014 | enhancement | SDM::CalcBetas | an option to pool all but the single-trial in question to simple regressors has been added to improve the stability of single trial betas | | |
| | | 04/10/2014 | enhancement | neuroelf_updatebuilds.m | the function now keeps correctly track of build number and date | | |
| | | 04/09/2014 | enhancement | PRT::CreateSDM | names for parametric regressors can now be provided, such that they occur properly in the regressor names and in the GLM output | changes also made in MDM::SDMs | |
| | | 04/06/2014 | enhancement | readeprimetextlog.m | now allows to return the result as a flat struct (instead of several sub-levels) | | |
| | | 04/04/2014 | enhancement | AFT::RenderToTransimg | added slice-ranges to calling syntax, so volumes can be "sliced" along the cardinal axes | | |
| | | 03/27/2014 | bug fix (MEX) | renderv3dxia.c | RGB-volumes would not be correctly sliced (interpolation code error) in one of the three slicing directions | | |
| | | 03/27/2014 | enhancement (GUI) | ne_smoothstats.m | this function is now also directly available via the VMP menu | prior to this change, the rendering dialog was necessary | |
| | | 03/20/2014 | enhancement (GUI) | neureolf_gui | the rendering view can now be undocked, which allows arbitrary image size (incl. non-square) | | |
| | | 03/13/2014 | new GUI feature | ne_vmr_exportrgb.m | allows to export a VMR into an RGB-volume Nifti file, which then allows colored drawing | | |
| | | 03/13/2014 | pre-release | NeuroElf | pre-release of v0.9d | | |
| | ==== Release v0.9c (04/29/2011 through 03/13/2014) ==== |
| | ^ Date of change ^ Type of change ^ Changed Object ^ Description ^ Comments ^ |
| | | 03/12/2014 | enhancement | AFT::GetVolume | if a cluster-size threshold was enforced, the volume can be masked with the resulting binary volume | | |
| | | 03/11/2014 | enhancement | renderv3d.m, AFT::RenderToTransimg | added statistical overlay (inlay) to the 3D rendering engine, as well as RGB-volume rendering | | |
| | | 03/10/2014 | enhancement (GUI) | neuroelf_gui | now support for 2D/3D RGB drawing in the drawing mode | | |
| | | 03/07/2014 | enhancement | AFT::ClusterTable | small-volume-correction (SVC) has been added to the cluster table method (only for VMPs that store the smoothness information) | the SVC-corrected map is stored in a new Map in the VMP on which it is called | |
| | | 03/06/2014 | enhancement | xffmethods.m | methods are now stored as function handles, which speeds up calls to OBJ::Method code a bit further | | |
| | | 03/05/2014 | enhancement | renderv3d.m, AFT::RenderToTransimg | added the alpha blending option to the rendering enging | | |
| | | 03/04/2014 | enhancement | @xff/private/*.m | replaced the (relatively costly) call to isxff(...) with a private function | this change applies to all OBJ::Method calls | |
| | | 03/01/2014 | bug fix (xff code) | SDM::Concatenate | a problem could occur if the confounds didn't contain a constant | | |
| | | 02/28/2014 | new GUI feature | neuroelf_gui | next to the slow slice-wise rendering, a new rendering feature (using Dirk-Jan Kroon's BSD-licensed code) is available to perform rendering in the main UI | | |
| | | 02/26/2014 | new functions | renderv3d.m | implementation of Dirk-Jan Kroon's rendering code in NeuroElf | in addition, some other functions have been created containing some auxiliary code | |
| | | 02/17/2014 | enhancement | PRT::CreateSDM | a warning is printed for every onset that is out of bounds (has no effect on regressors) | this is useful to detect problems with PRT-generation scripts or wrong VTC assignment | |
| | | 01/31/2014 | enhancement | dcm2nii.m | added Chris Rorden's DICOM-2-Nifti conversion tool as an option | this highly improves speed of the conversion process for one-file-per-slice DICOM sets | |
| | | 01/28/2014 | enhancement | asciiread.m | Unicode files are now autodetected (only works for reading files) | | |
| | | 01/22/2014 | new GUI feature | neuroelf_gui | if exactly two statistical maps are overlayed, a special joining modus can be selected that shows overlap in the maximally distant-hue color | | |
| | | 01/22/2014 | new function | maxdistcol.m | compute the maximally distant-hue color for a set of color pairs | | |
| | | 01/14/2014 | enhancement | VOI::ImportClusters | method now also supports compressed Nifti files as inputs | | |
| | | 12/21/2013 | enhancement | conjval.m, conjvalp.m | allows a new calling syntax, such that the conjunction is computed over a dimension in the input data, whereas the second argument **must** then signify the dimension | | |
| | | 12/04/2013 | new xff method | SRF::NeighborsNDegree | return the list of neighbors up to a certain degree | | |
| | | 11/27/2013 | new GUI feature | ne_render.m | added capability to generate slice-update movies from rendering | | |
| | | 11/14/2013 | enhancement | smoothdata3.m | also allows to use FFT and iFFT based smoothing (faster for large number of volumes) | | |
| | | 11/14/2013 | enhancement | @transio/transio.m | if a file cannot be opened for reading due to locking (FILE IN USE), transio will re-try up to 5 times with increasing pauses with a total of 1.6 seconds waiting time max | this was added to allow brief times of file-locking for other processes, as once a transio access is completed, the corresponding file pointer is closed again | |
| | | 11/14/2013 | enhancement | alphasim.m | instead of using re-scaled random data, now also allows to create (more accurate) t-maps from smoothed random maps | this increases the accuracy, particularly for very low D.F. maps | |
| | | 11/07/2013 | enhancement | MDM::ComputeGLM | added option to write out residual after regression of known effects | | |
| | | 11/06/2013 | enhancement | importvtcfromanalyze | attempts to automatically load the realignment parameters found in the directory of the data into the RunTimeVars structure of the VTC | | |
| | | 11/04/2013 | enhancement | VMP::ImportSPMMaps | if SPM-t maps are imported, the method also attempts to import the estimate of the smoothness of the residual (RPV.hdr/img) | | |
| | | 10/24/2013 | bug fix (xff code) | AFT::SliceToTransimg | erroneously marked some VMR voxels as being colored | due to minimal rounding errors in flexinterpn.c MEX, values that are 225 can come out as the next higher double precision value | |
| | | 09/16/2013 | enhancement (GUI) | ne_cm_compute.m | the contrast manager now supports running multiple selected contrasts (instead of just either one or all) | | |
| | | 09/05/2013 | enhancement | MDM::ComputeGLM | added automatic global signal extraction from colin-brain based GM/WM/CSF regions (conservative estimates) | this feature is available for standard-bounding-box data with either 2 or 3mm resolution | |
| | | 08/14/2013 | enhancement | SDM::CalcBetas | now supports MTC+SSM combination as inputs | | |
| | | 07/19/2013 | enhancement (GUI) | neuroelf_gui | new option that allows to turn subject IDs off when VOI betas are extracted from clusters | | |
| | | 07/07/2013 | enhancement | MDM::VOITimeCourses | extended to allow POIs for MTC-based MDMs | | |
| | | 07/06/2013 | enhancement | GLM::VOIBetas | now allows a list of coordinates to be passed in to extract values from a single VOI (or voxel) | | |
| | | 07/06/2013 | bug fix (xff code) | MDM::ComputeGLM | for MTC-based GLMs, an error occurred for RFX computations | | |
| | | 05/20/2013 | new function | vifactor.m | compute the variance-inflation factor (VIF) for regressors of a design matrix | | |
| | | 05/08/2013 | enhancement (GUI) | neuroelf_gui | added compressed Nifti files (*.nii.gz) to the file selector for statistical maps | | |
| | | 05/03/2013 | enhancement | GLM::RFX_rMap, GLM::RFX_tMap | in addition to the estimated overall smoothness of the map now also stores the actual smoothness images | this is as a preparatory step for small-volume-correction based on the actual number of resels in a particular volume | |
| | | 05/01/2013 | new GUI feature | spm5_preprojobs | added the option to brain-extract anatomical scans to improve coregistration with the functional data | | |
| | | 04/30/2013 | new function | spm5_extract_brain | command line tool loading a pre-defined job and using SPM's segmentation to extract the brain from an anatomical dataset | | |
| | | 04/25/2013 | enhancement | AFT::Browse | for VMP objects (and other objects with maps), the map number can now be given in the call, e.g. ''vmp.Browse(3);'' | | |
| | | 04/19/2013 | bug fix (xff code) | MDM::ConditionOnsets | this now takes the ''.tshift'' parameter correctly into account to allow (command-line based) shifting of onsets for methods such as MDM::VOICondAverage | | |
| | | 04/18/2013 | enhancement | @xff/subsref.m | methods (but not fieldnames) can now be abbreviated if there is only one unique continuation | example: ''obj.Bro;'' will call AFT::Browse | |
| | | 04/15/2013 | enhancement | VTC::CreateMTC | added sinc interpolation as option when creating MTCs | | |
| | | 04/15/2013 | added feature | MDM::VTCCondAverage | creates whole-brain onset-locked averages in arbitrary (virtual) TRs to visualize trial-/condition-based time courses for each location in the brain | additional functionality is provided with VTC::AverageMovieVMP, VTC::AveragePeak, VTC::CombineAvgVTCs, and VTC::JoinAvgTCs | |
| | | 04/12/2013 | enhancement | @xprogress | figures and axes and now created with HandleVisibility set to '''off''' to prevent random axis plotting into them | | |
| | | 04/03/2013 | enhancements | PLP::MKDA | several smaller enhancements to MKDA code (allowing to fix coordinates to integer values and also specify an inputmask | | |
| | | 03/07/2013 | new function | generatetdx.m | generate a design matrix X based on tabular data with lookups | | |
| | | 03/03/2013 | enhancement (MEX) | histcount.c | now the input data can also be weighted to generate a weighted histogram | | |
| | | 02/28/2013 | new functions | modelcomp.m, modelcompse.m | computes an F-statistic (also for N-d data), comparing two models (full and reduced) | | |
| | | 02/22/2013 | enhancement | fitrobustbisquare_img.m | added support for passing in preliminary/prior weights | | |
| | | 02/20/2013 | added feature | MDM::ComputeGLM | now supports using Vince Calhoun's HRFboost code (implemented separately) | also affected are MDM::SDMs and PRT::CreateSDM, also returning the basis function set | |
| | | 02/18/2013 | enhancement (format) | GLM.bff | the AR1Pre and AR1Post fields have been renamed to ARPre and ARPost | this is to reflect the fact that BVQX GLMs now support AR(2) models | |
| | | 02/18/2013 | new file format | DTA.bff | added support for STATA (file version 113 through 115) files | | |
| | | 02/06/2013 | enhancement | createfmr.m | improved MOSAIC detection | | |
| | | 02/02/2013 | enhancement | glmtstat.m | allows robust weights to be added to compute general t-statistics | | |
| | | 02/02/2013 | enhancement (MEX) | cov_nd.c | added support for auto-correlation (lag) and cov/corr computation along first dimensions | | |
| | | 02/02/2013 | new xff method | PLP::TDDLabelGM | inquire Talairach Daemon Database labels for points | | |
| | | 01/31/2013 | enhancement (format) | VMP.bff | added support for FileVersion 1 (first-ever) VMPs | | |
| | | 01/29/2013 | enhancement | ac2vmp.m | additional support for cluster files from Tor Wager's tools | | |
| | | 01/28/2013 | new function | dispp.m | convenience/shortcut function calling first ''disp(...)'' and then ''pause(0.001);'' to force-refresh the output | | |
| | | 01/26/2013 | enhancement | PLP::Select | a mask can now be specified as a second argument next to the selection condition, and points outside the mask are then removed | | |
| | | 01/26/2013 | enhancement | PLP::PlotOnSlice | this method now returns the handles of points and texts so they can be manipulated later (e.g. re-sized or deleted) | | |
| | | 01/08/2013 | enhancement | VOI::CreateMSK | instead of supplying a MSK object, also a HDR/NII object can be specified to create SPM-compatible masks | | |
| | | 12/18/2012 | enhancement | psctrans.m, ztrans.m | speed increase over previous implementation | | |
| | | 12/14/2012 | enhancement | AFT::GetVolume | added support for accessing global maps from FFX-GLMs (with map number after all betas + XY maps) | the order of additional maps is ''MultipleRegressionR'', ''MCorrSS'', ''TimeCourseMean'', and then all ''ARLag'' maps | |
| | | 12/13/2012 | enhancement | GLM::FFX_tMap | emulate BrainVoyager's AR(1) modeling when computing FFX-based t-Maps | this is very preliminary and requires additional testing! | |
| | | 12/12/2012 | enhancement | AFT::ExportNifti | an additional argument, ''talorder'', can be given to force the major axes being in Talairach/MNI order and orientation | | |
| | | 12/12/2012 | new function | image_matchprops.m | match several images on several properies (contrast, luminance, size, etc.) | | |
| | | 12/06/2012 | enhancement | GLM::RFX_conmaps | added support for FFX-GLMs when calling the RFX_conmaps method | | |
| | | 12/04/2012 | enhancement/fix | splitclustercoords.m | now the distance to the central point is taken into account, improving the general splitting of clusters into more realistic sub-units | | |
| | | 12/04/2012 | enhancement | @xff/isfield.m | xff objects now support the isfield function (as a struct) to check whether a field exists | | |
| | | 11/27/2012 | enhancement/fix | GLM::RemoveSubject | prior to the fix, this method would remove all subjects starting with the same string (e.g. removing ''SUB10'' would also remove ''SUB105'') | | |
| | | 11/07/2012 | enhancement | @xfigure/xfigure | to improve performance, properties and methods that are used more frequently are tested for first in the switch/case construction | | |
| | | 10/17/2012 | enhancement | GLM::RFX_tMaps | automatically filters out subjects for which a contrast map (weighted sum of beta maps) contains NaN values due to missing conditions | the degrees of freedom will be adjusted correctly! | |
| | | 10/12/2012 | new GUI feature | neuroelf_gui | added NeuroSynth maps to the GUI's File menu | | |
| | | 10/04/2012 | new xff method | MTC::SmoothnessSMP | compute statistical map showing the estimated smoothness of an (residual) MTC | | |
| | | 09/27/2012 | enhancement | HDR::InhomogeneityCorrect | now supports passing in an additional binary mask to prevent known voxels outside the brain to be taken into the estimate | | |
| | | 09/19/2012 | new function | importrfxglmfromafni.m | added function to generate a NeuroElf/BVQX compatible GLM file out of a series of AFNI HEAD/BRIK regression outputs | | |
| | | 09/19/2012 | enhancement | VMP::ImportSPMMaps | now also supports importing from HEAD/BRIK files | | |
| | | 09/14/2012 | enhancement | VMP::PerformFDR | this method now takes the estimated smoothness into account to compute the number of maximum resels for the required Bonferroni level | | |
| | | 09/07/2012 | new GUI feature | ne_glmbetaplot.m | added checkbox to display general info (location, number of voxels, number of subjects) as title | | |
| | | 08/15/2012 | enhancement | alphasim.m | reflecting the multiple linear regression capabilities of GLM::RFX_rMap, alphasim now supports combining several regressors into one model when computing false positive rates | | |
| | | 07/30/2012 | enhancement (GUI) | fmriqasheet.m | now allows to display noise estimate from individual slices when clicking into the time course | | |
| | | 07/25/2012 | enhancement (GUI) | ne_vmp_createsmp.m | if no surfaces are loaded, a set of default surfaces (LH+RH for the 40k vertices colin brains) are suggested to be loaded | | |
| | | 07/15/2012 | enhancement (GUI) | neuroelf_gui | the option to check fMRI quality now also allows to load existing output files of the fmriquality.m function | | |
| | | 06/25/2012 | enhancement | calcbetas.m | added features: AR(1) and (pre-computed!) weights can be specified as arguments | | |
| | | 05/08/2012 | new GUI feature | ne_cm_compute.m | now instead of comparing groups, maps for groups separately can be computed for visual inspection | | |
| | | 05/01/2012 | enhancement | acsvread.m | numeric conversion now restricts the number of output values to prevent invalid numbers | | |
| | | 05/01/2012 | added feature | xff / bffio.m | added support for gzip-compressed files | for files with transio access (HDR/NII), the content will be temporarily unpacked into the system ''TEMP'' folder | |
| | | 04/26/2012 | added function | hrfboost.m | implementation of Vince Calhoun's HRFboost algorithm | | |
| | | 04/17/2012 | bug fix (xff code) | VMP::ComputeFormula | if the ''.MapParameter'' field is set, it is also expanded if necessary to avoid invalid objects after saving | | |
| | | 03/15/2012 | enhancement | colorpicker.m | the function now also returns a second output informing the calling function whether the dialog was canceled or not | this helps to determine whether a UI update is needed | |
| | | 03/15/2012 | enhancement (GUI) | mkda.tfg | added several options to the MKDA UI menu, incl. plot on slice and plot on surface | | |
| | | 02/28/2012 | enhancement | @xff/private/xffrequestfile.m | the generic file requestor upon using ''obj = xff('*.EXT');'' can now be used to select files with different extensions by placing them in parentheses, split by the pipe character | example: ''stats = xff('*.(glm|vmp)');'' | |
| | | 02/28/2012 | new xff method | HDR::SliceTiming | added slice-timing to NeuroElf directly | this method does not use SPM code | |
| | | 02/24/2012 | new xff method | AFT::TimeCourseCorr | compute slice-based cross-correlation matrix | this can be used to guess for interleaving distance for slice-timing (as a confirmation) | |
| | | 02/03/2012 | new GUI feature | ne_remote.m | added remote-control support via HTTP/HTML connection | this can also be used to serve VMP content to a web browser | |
| | | 01/24/2012 | enhancement (GUI) | ne_satresize.m | slice-based satellites now can be resized with the underlying transio object being recreated in a higher resolution | | |
| | | 01/24/2012 | enhancement (format) | TAL.tff | FileVersion 2 with added fields is now supported | | |
| | | 01/24/2012 | bug fix (xff code) | VOI::ApplyTrf | if the VOI object contained more than one VOI field, the code would not correctly allocate the memory, resulting in slower performance | | |
| | | 01/23/2012 | enhancement | renamedicom.m | added capability to first pack all DICOM files into a cell array to increase speed | this requires fewer file-system calls when re-reading the directory after every rename operation | |
| | | 01/22/2012 | enhancement | @transimg/*.m | the transimg class now allows to add partial and transformed layers | | |
| | 01/13/2012 | enhancement (GUI) | ne_maskstatswithvmr.m | will use the transio-loading feature to ensure that GLMs with data on disk only will not be altered | | | | 01/13/2012 | enhancement (GUI) | ne_maskstatswithvmr.m | will use the transio-loading feature to ensure that GLMs with data on disk only will not be altered | | |
| | 01/13/2012 | new xff method | AFT::LoadTransIOData | allows to read all transio objects into memory in any xff object | this is particularly useful for GLM files, as the exact fieldnames need not be specified | | | 01/13/2012 | new xff method | AFT::LoadTransIOData | allows to read all transio objects into memory in any xff object | this is particularly useful for GLM files, as the exact fieldnames need not be specified | |
