SnPM13: Bugs & Fixes This file describes the bugs that have been reported, along with the appropriate fixes. Updated versions of appropriate SnPM functions are available from in the snpm13_updates: http://warwick.ac.uk/snpm/distribution/snpm13_updates --- SnPM 13.1.06 --- * fix: ANOVA between group "all zero"/"all equal" options were flipped in the menu of the matlabbatch. * fix: snpm_cp can now handle XYZ locations in a 1D space. * Version 13.1.06 (`snpm`) --- SnPM 13.1.05 --- * fix: two-sample t-test with nscans>12 was errored due to call to undefined variable `nPerm` (bug introduced in previous release: 13.1.4) (`snpm_pi_TwoSampT`) * fix: warning on size of `SnPM_ST.mat` was never raised * Add seed shuffling for paired two-sample test modules (`snpm_pi_PairT`, `snpm_pi_PairTrand`) * Version 13.1.05 (`snpm`) --- SnPM 13.1.04 --- * snpm SnPM version 13.1.04 * snpm_bch_ui, snpm_cp, snpm_ui Fix: implicit masking for non-float datatypes * snpm_pi_ANOVAbtwnS, snpm_pi_ANOVAwithinS, snpm_pi_Corr, snpm_pi_Corr1S, snpm_pi_OneSampT, snpm_pi_TwoSampPairT, snpm_pi_TwoSampT, snpm_pi_TwoSampTss Update syntax to set the seed of the random number generator (rng) * snpm_defaults New SnPM global parameter shuffle_seed. If true, the rng uses a 'shuffle' seed providing different results for each run. If false Matlab's 'default' seed or any seed defined by the user will be used . * snpm_pi_TwoSampT Allows MC permutation (with reptitions) for large enough nPerms * snpm_pp, snpm_ui Do not display figures in command-line mode * snpm, snpm_check_nperm, snpm_combo, snpm_cp, snpm_init, snpm_pi_ANOVAbtwnS, snpm_pi_ANOVAwithinS, snpm_pi_Corr, snpm_pi_Corr1S, snpm_pi_OneSampT, snpm_pi_PairT, snpm_pi_PairTrand, snpm_pi_TwoSampPairT, snpm_pi_TwoSampT, snpm_pi_TwoSampTss, snpm_pp, snpm_t2z, snpm_uc_FDR, snpm_ui, spm_append_96 Add identifiers to errors and warnings * snpm_cp Fix: Do not assume statistic is T when computing cluster forming threshold from P-value * generic_test_snpm, skeleton_class, test_ANOVAbetween, test_multisub_withinsubanova, test_multisubpaired2cond, test_multisubsimpleregression, test_oneSample, test_onesub_regression, test_onesub_twocondrepl, test_twoSample, test_twosample_twocond Test in command-line mode with no shuffling for the random seed, using new rng syntax. --- Updates from SnPM 13.1.03 --- * snpm SnPM version 13.1.03 * snpm_pi_PairT Now allows more than 52 subjects, as previously that would generate a "Maximum variable size allowed by the program" error message. --- Updates from SnPM 13.1.02 --- * snpm SnPM version 13.1.02 * snpm_pp, snpm_combo_pp Update contrast display for compatibility with Matlab R2014b. * generic_test_snpm Updates affecting tests only. --- Updates from SnPM 13.1.01 --- * snpm SnPM version 13.1.01 * snpm_pp Check that 'Locs_vox' is integer according to a pre-defined tolerance level (as in snpm_cp). --- Updates from SnPM13.1.00 --- * snpm_cp, snpm_pp, generic_test_snpm, test_oneSample Cluster-forming threshold defined by a P-value are now extended to pseudo-T statistic (with variance smoothing). The Z-score corresponding to the selected P-value is used as an approximation of pseudo-T values. --- Updates from SnPM13.0.14 --- * snpm_bch_ui_Corr, snpm_bch_ui_Corr1S, snpm_pi_Corr, snpm_pi_Corr1S, test_multisubsimpleregression, test_onesub_regression Introduce nuisance covariates in simple-subject and multi-subject regressions. --- Updates from SnPM13.0.13 --- * snpm_combo_pp Fix: Set bNeg to 0 for F-tests. --- Updates from SnPM13.0.12 --- * snpm_pi_OneSampT Fix: Added new random mode for sampling of sign flips (Above 53 scans the binary-coding fails as Matlab's double significand runs out of precision). --- Updates from SnPM13.0.11 --- * snpm_ui Fix: When relative thresholding is set, then global calculation (user defined or mean) must be computed. * snpm_pi_TwoSampPairT, snpm_pi_TwoSampT Fix: Unbalanced two-sample tests were wrongly aborted. * test_multisubpaired2cond, test_oneSample, test_twoSample, test_twosample_twocond Updates affecting tests only. --- Updates from SnPM13.0.10 --- * snpm_ui Fix: ANCOVA normalisation (with an image presenting negative mean using spm_globals). --- Updates from SnPM13.09 --- * snpm_cp Increase tolerance in checking that 'Locs_vox' is integer. --- Updates from SnPM13.08 --- * snpm_cp, spm_append_96 Display warning message if SnPM_ST file becomes very large. Display more meaningful error message when Locs_vox is not interger. * snpm_pp Display warning message if SnPM_ST can not be loaded. --- Updates from SnPM13.07 --- * snpm For backward-compatibility, open SPM batch window and display where to find SnPM tools when 'snpm' in called at the Matlab prompt. * snpm_pp Fix: slow cluster inference with variance smoothing. * generic_test_snpm, test_oneSample, test_twoSample Updates affecting tests only. --- Updates from SnPM13.06 --- * snpm_ui Apply user-defined scaling. * generic_test_snpm, test_oneSample, test_onesub_twocondrepl, test_twoSample Updates affecting tests only. --- Updates from SnPM13.05 --- * snpm_STcalc Cluster labels from spm_max are not necessarily continuous. * snpm_pi_ANOVAbtwnS, snpm_pi_ANOVAwithinS, snpm_pi_Corr, snpm_pi_Corr1S, snpm_pi_OneSampT, snpm_pi_PairT, snpm_pi_TwoSampPairT, snpm_pi_TwoSampT, snpm_pi_TwoSampTss Fix: if number of requested permutations is equal to the maximum number of possible permutations. * snpm_pi_TwoSampTss, snpm_pi_TwoSampPairT, snpm_pi_TwoSampT Compute possible permutations (PiCond) in a more efficient way to avoid potential memory faults for large groups. --- Updates from SnPM13.04 --- * snpm_ui Apply absolute and relative masking. --- Updates from SnPM13.03 --- * snpm_pi_TwoSampT Compute possible permutations (PiCond) in a more efficient way to avoid potential memory faults for large groups. --- Updates from SnPM13.02 --- * snpm_pp Fix: if the extension is missing in the provided result file name, use .nii by default. Use NaNs in thresholded map background instead of zeros. * [deleted spm_SnPM13] SnPM is now only accessible through the Batch window (SPM -> Tools -> SnPM). * snpm_pi_ANOVAbtwnS, snpm_pi_ANOVAwithinS, snpm_pi_Corr1S, snpm_pi_OneSampT, snpm_pi_PairT, snpm_pi_TwoSampPairT, snpm_pi_TwoSampT Minor update in the display. * test/ Miror corrections affecting tests procedure only. --- Updates from SnPM13.01 --- * snpm_cp Synopsis: When half the permutations are computed (i.e. bhPerms is true) and StartPerm is 2 then the initial number of permutation could be 2 depending on sign of T0. * snpm_test_config, snpm_test_gound_truth and generic_test_snpm Miror corrections affecting tests procedure only.