Version 2.2.2

Changes made since the previous version (v2.2.1)

• fix: Remove dependence on old spm_matlab_version_chk #183
• fix: Removing references to Gaussian Random Field Theory #180
• fix: Fix a bug related to the progress display of parametric analyses #179
• fix: Remove use of double quotes to improve Matlab version compatibility #181

Links to relevant issues

Issue #165
Issue #169

Version 2.2.1

Changes made since the previous version (v2.2.0)

• enh: modify the way non-parametric cluster-wise inference is performed for all types of inputs by using, when possible, Box-Cox normalized cluster extents instead of traditional cluster extents
• enh: remove the possibility to Box-Cox normalize the cluster extents using the mean and the standard deviation of the Box-Cox transformed cluster extents
• enh: add helper functions related to the Box-Cox normalization
• enh: invert the order of the sub-options for cluster-wise inference
• enh: add an option allowing the user to add a surface area file for GIfTI inputs
• enh: update some function headers
• enh: replace some recent Matlab functions or syntaxes to enable the compatibility of the SwE toolbox with old Matlab versions
• enh: use a consistent naming for .mat results across parametric and non-parametric analyses
• enh: improve the helper text of some options of the SwE model specification batch module
• enh: display a more visually appealing version of the design matrix in the result display window
• enh: improve the specification of t- and f-contrasts for Wild Bootstrap analyses
• fix: fix a bug occurring when a chunk of data would be entirely masked out
• fix: fix a bug occurring when writing GIfTI files in Octave
• fix: fix a bug related to the automatic masking of CIfTI and GIfTI analyses
• fix: fix a bug in the computation of X-scores for .mat inputs
• fix: fix a bug for .mat inputs where spm_mesh_detect would not work for empty cell arrays
• fix: fix a bug where some results for .mat analyses would not be saved correctly
• fix: fix a bug occurring because the dense scalar CIfTI intent code would not be recognized by the toolbox
• fix: fix a bug occurring when reading CIfTI file in Octave
• dev: add new tests that are covering CIfTI and GIfTI inputs
• dev: clean up several pieces of code (e.g., fix indentation inconsistencies, remove commented/unused pieces of code, rename variables, refactor the computation of cluster statistics, remove trailing tabs and spaces, add a final newline if missing,...)

Link to relevant issues

• Issue #41
• Issue #161
• Issue #163
• Issue #168
• Issue #171
• Issue #173
• Issue #176

Version 2.2.0

Changes made since the previous version (v2.1.1)

• enh: add GIfTI support
• enh: add CIfTI support
• enh: all the non-parametric WB p-values are now computed using a tolerance of 10^-8 for comparing real numbers
• enh: the maximum TFCE scores are now saved into SwE.mat
• enh: the WB procedure now makes voxel-wise inference on Z or X instead of T or Z (the main reason for this is to be consistent with cluster-wise inference which forms clusters based on Z or X)
• enh: improve the thresholding description in the result display
• enh: add a new function swe_compareVersions able to compare versions of the toolbox
• enh: add a (hidden) way to supply a WB resampling matrix instead of letting the toolbox generate one by itself
• enh: add the effective number of degrees of freedom Approximation I for the WB
• enh: replace the loop over planes by a loop over chunks of data
• enh: improve the way some X-scores are computed in order to prevent Inf values
• enh: add the option to constrain volume clusters to be within the ROI boundaries in CIfTI analyses
• enh: modify the naming convention for CIfTI, GIfTI and .mat outputs to better match PALM naming convention
• fix: the p-value thresholding is now inclusive for WB analyses
• fix: for WB analyses, the p-values displayed are systematically the WB p-values instead of the parametric p-values
• fix: fix a result display error observed for the classic parametric SwE
• fix: fix some typos
• fix: fix some bugs in the progress display and improve it
• fix: fix several bugs in the result display GUI
• fix: ensure that each CIfTI outputs contain an appropriate CIfTI XML file
• fix: replace the nan values in output files by zero values (this is to avoid issues when reading the CIfTI outputs in other software packages)
• fix: keep only one "NameMap" in the XML extension of the toolbox dscalar.nii outputs
• fix: fix bugs related to zeroing nan values
• fix: fix several bugs related to the naive estimation of the effective number of degrees of freedom
• fix: fix a bug in the detection of sub-design matrices
• fix: fix a bug where some ROI volume labels with multiple 'V_' would not be processed correctly

Link to relevant issues

• Issue #5
• Issue #41
• Issue #102
• Issue #107
• Issue #121
• Issue #122
• Issue #123
• Issue #124
• Issue #132
• issue #140
• issue #148
• issue #150
• issue #153
• issue #154
• issue #156

Version 2.2.0.rc2 (Release Candidate)

Changes made since the previous version

• fix: ensure that each CIfTI output contains an appropriate CIfTI XML file
• fix: replace the nan values in output files by zero values (this is to avoid issues when reading the CIfTI outputs in other software packages)

Version 2.2.0.rc (Release Candidate)

Changes made since the previous version

• enh: add GIfTI support
• enh: add CIfTI support
• enh: all the non-parametric WB p-values are now computed using a tolerance of 10^-8 for comparing real numbers
• enh: the maximum TFCE scores are now saved into SwE.mat
• enh: the WB procedure now makes voxel-wise inference on Z or X instead of T or Z (the main reason for this is to be consistent with cluster-wise inference which forms clusters based on Z or X)
• enh: improve the thresholding description in the result display
• enh: add a new function swe_compareVersions able to compare versions of the toolbox
• enh: add a (hidden) way to supply a WB resampling matrix instead of letting the toolbox generate one by itself
• enh: add the effective number of degrees of freedom Approximation I for the WB
• enh: replace the loop over planes by a loop over chunks of data
• enh: improve the way some X-scores are computed in order to prevent Inf values
• fix: the p-value thresholding is now inclusive for WB analyses
• fix: for WB analyses, the p-values displayed are systematically the WB p-values instead of the parametric p-values
• fix: fix a result display error observed for the classic parametric SwE
• fix: fix some typos
• fix: fix some bugs in the progress display and improve it
• fix: fix several bugs in the result display GUI

Link to relevant issues

• Issue #5
• Issue #41
• Issue #102
• Issue #107
• Issue #121
• Issue #122
• Issue #123
• Issue #124
• Issue #132

Version 2.1.1

Changes made since the previous version

• fix: Handle correctly the case dof_type = 0 for Wild Bootstrap
• fix: Make the new version of the SwE scan selection dialogue compatible with SPM8
• fix: Fix a status message display for conjunctions
• fix: Fix a bug in subfunction swe_resid_corr for dof_type = 1 (before, it would throw an error)
• fix: The subfunction swe_hyptest sets now the p-value of F-Score <= 0 to 1
• fix: The bootstrapped TFCE scores for F-contrasts are now computed based on Z-scores instead of X-scores
• fix: Compute correctly the surviving voxels of each bootstrap of the cluster-wise WB for negative effects
• fix: Fix the post-hoc masking for parametric tests which was not masking any voxels anymore
• fix: Fix the results display of clusterwise Wild Bootstrap for negative contrasts which would sometimes use the voxels surviving the activation (i.e. positive contrast)
• fix: Display correctly the 95th percentiles of maximum scores and maximum cluster sizes for negative t-contrasts (before, those of the positive t-contrasts were displayed)
• fix: Fix some errors in the Contrasts menu in the display window (before, clicking on some buttons in this menu would crash the toolbox)
• enh: save the xCon field in SwE.mat for Wild Bootstrap analyses
• enh: Prevent some Z-scores to be infinite
• enh: Improve the function swe_update by adding the possibility to use webread instead of urlread if the latter fails to fetch the most recent release version
• enh: Fix some typos

Link to relevant issues

• Issue #99
• Issue #103
• Issue #107
• Issue #111
• Issue #112
• Issue #116
• Issue #122

Version 2.1.0

Changes made since previous version

• enh: The eigenvariates display now works.
• enh: The code now checks for incompatibilities when loading the SwE.mat file.
• fix: Random number generator to use is now specified.
• dev: Identifiers have been added to the headers of all files.
• enh: Display options are now available for deactivations in a wild bootstrap analysis.
• dev: Indentation has been reviewed for several of the files.

Link to relevant issues

• Issue #1
• Issue #69
• Issue #86
• Issue #89
• Issue #92

Version 2.0.0

Changes made since previous version

• enh: TFCE added.
• enh: Added swe_update function.
• dev: Detailed comment review of all functions.
• enh: Allowed users to specify mutliple covariates from one file.
• enh: Updated GUI with batch system integration.
• enh: Small volume corrections for display.
• fix: Memory usage for large TFCE split into blocks.
• fix: Classic analyses bugs.
• fix: Setting of SPM modality correctly.
• fix: (Limited) Matlab 2016b compatibility (Not supported in general).
• fix: Seeds set randomly.

Link to relevant issues

• Issue #14
• Issue #21
• Issue #25
• Issue #29
• Issue #40
• Issue #51
• Issue #63
• Issue #64
• Issue #68
• Issue #74

Version 2.0.0-rc (Release Candidate)

Changes made since previous version

• enh: Added swe_update function.
• dev: Detailed comment review of all functions.
• enh: Allowed users to specify mutliple covariates from one file.
• enh: Updated GUI with batch system integration.
• enh: Small volume corrections for display.

Link to relevant issues

• Issue #14
• Issue #21
• Issue #25
• Issue #29
• Issue #40
• Issue #51
• Issue #64

Version 1.2.11

Changes made since previous version

• fix: The error message given when no voxels remain after thresholding has been changed.
• fix: The bug reported concerning voxfmt not existing when no voxels survive thresholding has been fixed.
• dev: A watermark has been added to the design display so that the Design window also displays the version number of the SwE toolbox release used to specify the design.
• fix: The design matrix latex interpreter has been added into this release as it should have been in new_release_1.2.10.

Link to relevant issues

• Issue #55