------------------------------------------------------------------------
TFCE 1.3 | r332 | 2026-07-14

IMPORTANT: this release changes the p-values that are reported. Both tail
approximations are enabled by default, so an analysis rerun with 1.3 will not
reproduce the 1.2 numbers in the tail of the distribution -- it will resolve
them further. See "Changed" below before you compare old and new results.

Added: Exact TFCE by a max-tree (component tree over a union-find). The integral
       is now evaluated in closed form instead of being summed over a ladder of
       thresholds, so there is no step size and no discretisation error. A
       stepped transform converges onto this one, halving its error with every
       doubling of the step count (1.7% at 100 steps, 0.8% at 200).
Added: Gamma tail approximation for FWE-corrected p-values. The distribution of
       the maximum is fitted by matching three moments, which resolves corrected
       p-values below the 1/n_perm floor of counting. Enabled by default
       (use_gamma_tail_approximation).
Added: Generalised Pareto tail approximation for uncorrected p-values, fitted by
       probability-weighted moments with the shape parameter pooled across
       elements. Resolves p-values below the counting floor and gives the same
       accuracy for roughly a fifth of the permutations. Enabled by default
       (use_pareto_tail_approximation).
Added: Sequential stopping (Besag-Clifford with a Gandy margin): stop permuting
       once every corrected p-value is pinned down. Opt-in, off by default
       (use_sequential_stopping in the batch GUI). About 6.5x fewer permutations
       on a null analysis.
Added: Batched TFCE mex (tfceMex_maxtree_batch) that transforms a block of
       permutations across threads.
Added: Voxel-wise F-contrasts for designs with a voxel-wise covariate.
Added: Validation suite, matlab/validation/run_all.m -- 105 checks covering the
       exactness of the transform, the tail fits, the sequential stopping rule,
       the nuisance methods, the fast GLM and the voxel-wise path.
Added: A warning when the permutation null is mis-calibrated, which catches a
       design that is not exchangeable the way the analysis assumes it is.
Added: A second implementation: a Python package (BSD-3) that compiles the same
       C core and is bit-identical to this toolbox. See python/ and README.md.

Changed: Corrected and uncorrected p-values below 1/n_perm are now extrapolated
       from a fitted tail instead of being floored. This is the change to be
       aware of when comparing against 1.2. Set use_gamma_tail_approximation and
       use_pareto_tail_approximation to false in tfce_estimate_stat.m to recover
       the old counting behaviour.
Changed: Removed the "Weighting of cluster size" option and its parameter. Saved
       batch jobs that set it will need it removed.
Changed: The permutation GLM no longer forms the permuted data. Under
       Freedman-Lane the residual-forming matrices cancel and the residual sum of
       squares can be updated directly, which is 4-8x faster and exact, not an
       approximation.
Changed: The voxel-wise covariate path is vectorised across voxels (17x).
Changed: The max-tree works in single precision and sorts by a radix sort on the
       raw float bit patterns rather than qsort (0.128 -> 0.081 s per
       permutation). Together with the batch mex this is about 2.5x.
Changed: The C core moved to c/ and is shared by both implementations. The MATLAB
       toolbox moved to matlab/. An installed toolbox is still a single flat
       folder, and compile.m finds the core in either layout.
Changed: The toolbox stays GPL-2.0-or-later. The C core and the Python package
       are BSD-3-Clause; neither contains SPM, SnPM or PALM code. See LICENSE.md.

Fixed: Surface analyses corrupted the heap and could crash MATLAB. GIFTI stores
       faces as int32 and the mex read them as double, so every vertex index was
       garbage. This affected every surface analysis, on every MATLAB version.
       Face indices are now read according to their actual type and are checked
       to be in range.
Fixed: A vertex with more than 26 neighbours overflowed a fixed-size buffer in
       the mesh neighbourhood lookup. Mesh degree is not bounded and is no longer
       assumed to be.
Fixed: With more than one covariate column, only the last one decided whether a
       contrast was permuted, which gave the wrong permutation scheme for the
       others.
Fixed: The variance shrinkage in the voxel-wise path collapsed to a no-op because
       the maximum was taken over a scalar inside the voxel loop instead of over
       the image.
Fixed: A Pareto fit could place a finite upper endpoint below the observed
       statistic and report p = 0. Fits the observation contradicts are rejected
       and fall back to the exponential.
Fixed: Degenerate voxel-wise designs were not detected, because an LU solve of a
       singular system returns large finite values rather than Inf or NaN. Rank
       is now tested with a Schur complement.

------------------------------------------------------------------------
The entries below are the Subversion log, from the initial import in 2010 up to
the move to git.
------------------------------------------------------------------------
r276 | gaser | 2024-07-08 21:02:45

Changed paths:
 M CHANGES.txt
 M cat_spm_results_ui.m
 M tfce_estimate_stat.m

Fixed: Added checks for additional cat-tools that should be ignored if CAT12
       is not installed.
------------------------------------------------------------------------
r273 | gaser | 2024-04-03 12:25:11

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Changed: Removed variance smoothing.
------------------------------------------------------------------------
r272 | gaser | 2024-04-03 12:19:39

Changed paths:
 M CHANGES.txt
 M cat_spm_results_ui.m
 M html/tfce.html
 M html/tfce.txt
 M tbx_cfg_tfce.m
 M tfceMex_pthread.c
 M tfce_estimate_stat.m

Changed: Removed bilateral filter that showed no improvement.
Changed: Removed option to change E_weight.
Changed: Added memore allocation check.
Changed: Use mat-format of SPM defaults for saving mat-files.
------------------------------------------------------------------------
r271 | gaser | 2023-08-18 18:38:19

Changed paths:
 M CHANGES.txt
 M spm_TFCE.m
 M tbx_cfg_tfce.m
 M tfce_estimate_stat.m

Changed: Updated function headers.
------------------------------------------------------------------------
r270 | gaser | 2023-05-12 08:37:15

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M html/tfce.html
 M old_tfce_results_ui.m
 M tfce_estimate_stat.m

Changed: Some minor cosmetic edits.
------------------------------------------------------------------------
r269 | gaser | 2023-05-11 15:14:21

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Changed: Added warning if covariates are found for longitudinal designs.
Changed: Added check that at least two time points are found for longitudinal 
         designs.
------------------------------------------------------------------------
r268 | gaser | 2023-05-04 13:55:32

Changed paths:
 M CHANGES.txt
 M cat_spm_results_ui.m
 M tfceMex_pthread.m

Fixed:   Corrected definition of contrast images when analysis folder was moved.
------------------------------------------------------------------------
r267 | gaser | 2023-04-17 10:21:02

Changed paths:
 M CHANGES.txt
 M tfceMex_pthread.m
 M tfceMex_pthread.mexmaca64
 M tfceMex_pthread.mexmaci64
 M tfce_estimate_stat.m
 M tfce_list.m
 M tfce_mesh.m
 M tfce_progress.m
 M tfce_surf_max.m
 M tfce_update.m

Changed: Modified header with author information.
------------------------------------------------------------------------
r266 | gaser | 2023-03-22 17:52:50

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m
 M tfce_getSPM.m

Fixed:   Corrected cat12-template path in tfce_estimate_stat.m and 
         tfce_getSPM.m.
------------------------------------------------------------------------
r265 | gaser | 2023-01-27 00:48:19

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M Makefile
 M cat_spm_results_ui.m
 M html/tfce.html
 M update_revision.sh

Changed: Updated cat_spm_results_ui.m from CAT12.
Changed: Removed unnecessary line in update_revision.sh.
Fixed:   Added "-O" flag to scp command in Makefile. 
------------------------------------------------------------------------
r264 | gaser | 2023-01-20 10:35:10

Changed paths:
 M CHANGES.txt
 M tfceMex_pthread.c
 M tfce_getSPM.m

Changed: Reformatted tfceMex_pthread.c
Changed: Added warning if SPM12 estimate function was used instead of CAT12
         Estimate Surface Models.
------------------------------------------------------------------------
r263 | gaser | 2023-01-12 17:57:57

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Changed: Added check whether permutation was already used because
         for some designs number of maximal permutations might differ.
------------------------------------------------------------------------
r261 | gaser | 2022-12-27 16:17:23

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Changed: Added new and hopefully faster pinv2 method that is also stable to
         tfce_estimate_stats.m. This method is based on faster svd function by
         Vipin Vijayan.
Changed: Added check for voxel-wise covariate which pinv methid is faster in
         tfce_estimate_stats.m.
------------------------------------------------------------------------
r260 | gaser | 2022-12-07 15:21:22

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Changed: Increased threshold when for disabling muli-threading.
------------------------------------------------------------------------
r259 | gaser | 2022-12-02 16:32:00

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M html/tfce.html
 M tfce_estimate_stat.m
 M tfce_progress.m

Changed: Again switched back to slower but more accuaret approach for voxel-wise 
         covariates.
Changed: Added pinv2 function that is much fast than Matlab builtin pinv.
Changed: Many smaller changes to increase speed for voxel-wise covariate.         
Deleted: Removed code from Chris Rorden that was not faster.
------------------------------------------------------------------------
r258 | gaser | 2022-12-02 16:31:16

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M html/tfce.html
 M tfce_estimate_stat.m
 M tfce_progress.m
D  tfce_pthread_ChrisRordan.c

Changed: Again switched back to slower but more accuaret approach for voxel-wise 
         covariates.
Changed: Added pinv2 function that is much fast than Matlab builtin pinv.
Changed: Many smaller changes to increase speed for voxel-wise covariate.         
Deleted: Removed code from Chris Rorden that was not faster.
------------------------------------------------------------------------
r256 | gaser | 2022-11-29 00:02:25

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M html/tfce.html
 M tfce_estimate_stat.m

Fixed: Corrected use of spm_Fcdf for F-statistic.
Fixed: Corrected use of additional mask with F-statistic.
------------------------------------------------------------------------
r255 | gaser | 2022-11-23 12:07:31

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M html/tfce.html
A  tfceMex_pthread.mexmaca64

Changed: Compiled mex-file for MACA64.
------------------------------------------------------------------------
r254 | gaser | 2022-11-11 00:01:44

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Changed: Added check for different mask images or missing absolute threshold or
         VBM analysis in tfce_estimate.m.
Changed: Modified ResMS (a form of shrinkage) to avoid problems of very low 
         variance as used in spm_spm.m
------------------------------------------------------------------------
r253 | gaser | 2022-11-09 21:56:55

Changed paths:
 M CHANGES.txt
 M tfce_update.m

Fixed: Corrected TFCE path.
------------------------------------------------------------------------
r251 | gaser | 2022-11-07 22:55:25

Changed paths:
MM CHANGES.txt

Changed: Updated toolbox paths.
Changed: Updated update function.
Added:   Created shell script to update revision number.
------------------------------------------------------------------------
r250 | gaser | 2022-11-07 22:55:04

Changed paths:
 M CHANGES.txt
M  Makefile
M  tfce_estimate_stat.m
M  tfce_getSPM.m
M  tfce_update.m

Changed: Updated toolbox paths.
Changed: Updated update function.
Added:   Created shell script to update revision number.
------------------------------------------------------------------------
r250 | gaser | 2022-11-07 22:54:02

Changed paths:
 M CHANGES.txt
 M Makefile
 M tfce_estimate_stat.m
 M tfce_getSPM.m
 M tfce_update.m

Changed: Updated toolbox paths.
Changed: Updated update function.
Added:   Created shell script to update revision number.
------------------------------------------------------------------------
r249 | gaser | 2022-11-07 22:53:15

Changed paths:
 M CHANGES.txt
 M Makefile
 M tfce_estimate_stat.m
 M tfce_getSPM.m
 M tfce_update.m
A  update_revision.sh

Changed: Updated toolbox paths.
Changed: Updated update function.
Added:   Created shell script to update revision number.
------------------------------------------------------------------------
r248 | gaser | 2022-10-05 00:48:15

Changed paths:
 M CHANGES.txt
 M Contents.m
 M INSTALL.txt
 M cat_spm_results_ui.m
 M html/tfce.html
 M spm_TFCE.m

Changed: Updated remaining hardcoded toolbox paths for TFCE.
-----------------------------------------------------------------------
r246 | gaser | 2022-08-19 16:29:30

Changed paths:
 M CHANGES.txt
 M tfce_estimate_stat.m

Fixed: Corrected check for voxelwise covariate.
------------------------------------------------------------------------
r234 | gaser | 2022-02-19 00:32:14

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Changed: Save unpermuted statistics before starting permutations.
------------------------------------------------------------------------
r233 | gaser | 2022-02-19 00:26:26 +0100 (Sat, 19 Feb 2022) | 9 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Changed: We assume that the null distribution will not change with voxel-wise 
         covariate and can therefore use the common design matrix without 
         voxel-wise covariates which is not that unbelievable slow.


------------------------------------------------------------------------
r232 | gaser | 2022-01-26 14:55:00 +0100 (Wed, 26 Jan 2022) | 8 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Fixed: Corrected bug for one-sample t-tests which lead to poor correlation to
       parametric statistics, but occured quite rarely.

------------------------------------------------------------------------
r231 | gaser | 2022-01-25 17:13:14 +0100 (Tue, 25 Jan 2022) | 7 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Fixed: Corrected handling of multiple defined contrasts.

------------------------------------------------------------------------
r230 | gaser | 2022-01-13 15:55:12 +0100 (Thu, 13 Jan 2022) | 8 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Fixed: Corrected check for multithreading performance that was not correctly
       working.        

------------------------------------------------------------------------
r229 | gaser | 2022-01-11 14:36:51 +0100 (Tue, 11 Jan 2022) | 8 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       html/tfce_FN.html
M       tfce_estimate_stat.m

Changed: Renamed maps for null distribution to nullT_*.

------------------------------------------------------------------------
r228 | gaser | 2022-01-11 14:20:14 +0100 (Tue, 11 Jan 2022) | 9 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       html/tfce_FN.html
M       tfce_estimate_stat.m

(1) Changed: Use option to save null distribution by default.
(2) Changed: Updated help text for filenames.           

------------------------------------------------------------------------
r227 | gaser | 2021-10-31 22:40:42 +0100 (Sun, 31 Oct 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Changed: Updated option to save null distribution as image.

------------------------------------------------------------------------
r226 | gaser | 2021-10-30 00:23:38 +0200 (Sat, 30 Oct 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Changed: Added hidden option to save null distribution.

------------------------------------------------------------------------
r225 | gaser | 2021-10-25 09:09:26 +0200 (Mon, 25 Oct 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

(2) Changed: If only one contrast is defined skip interactive selection for that.
(1) Fixed:   Added check for F-contrasts for effects of interest to 
             tfce_estimate_stat.m to correctly recognize number of 
             exchangeability blocks.
           

------------------------------------------------------------------------
r224 | gaser | 2021-10-22 16:34:05 +0200 (Fri, 22 Oct 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html
M       tfce_estimate_stat.m

(1) Changed: Updated check for installed atlases in cat_spm_results_ui.m.
(1) Fixed:   Corrected check for existing TFCE results in cat_spm_results_ui.m.
(2) Fixed:   Corrected check for multiple contrasts in tfce_estimate_stats.m.

------------------------------------------------------------------------
r223 | gaser | 2021-08-12 13:02:11 +0200 (Thu, 12 Aug 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html
M       tfce_estimate_stat.m

(1) Changed: Use a faster Freedman-Lane approach thanks to blog entry of Anderson 
             Winkler (https://brainder.org/2020/05/19/simplifying-freedman-lane).
(2) Fixed:  Corrected issues with non-existing VSPM field in tfce_stat_estimate.m.

------------------------------------------------------------------------
r222 | gaser | 2021-06-30 12:19:27 +0200 (Wed, 30 Jun 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m

Fixed: Corrected path if results are called from another folder in 
       cat_spm_results_ui.m.

------------------------------------------------------------------------
r221 | gaser | 2021-05-31 22:58:50 +0200 (Mon, 31 May 2021) | 5 lines

Changed paths:
M       CHANGES.txt

Changed: Allow voxel-wise covariate for longitudinal designs.

------------------------------------------------------------------------
r220 | gaser | 2021-05-30 19:24:34 +0200 (Sun, 30 May 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Changed: Allow voxel-wise covariate for longitudinal designs.

------------------------------------------------------------------------
r219 | gaser | 2021-04-30 17:48:52 +0200 (Fri, 30 Apr 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Changed: Shortened text in GUI window.

------------------------------------------------------------------------
r218 | gaser | 2021-04-30 17:47:20 +0200 (Fri, 30 Apr 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Fixed: Corrected handling of voxel-wise covariates for subsequent calls of 
       tfce_estimates.m

------------------------------------------------------------------------
r217 | gaser | 2021-04-23 00:14:31 +0200 (Fri, 23 Apr 2021) | 6 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Fixed: Corrected handling of parallel processing that ignored subsequent data.

------------------------------------------------------------------------
r216 | gaser | 2021-04-15 21:52:33 +0200 (Thu, 15 Apr 2021) | 10 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       html/tfce.html
M       tfce_estimate_stat.m

(1) Fixed:   Corrected check whether design should be estimated.
(2) Changed: Updated Makefile.


------------------------------------------------------------------------
r215 | gaser | 2021-04-15 19:48:39 +0200 (Thu, 15 Apr 2021) | 11 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html
M       tbx_cfg_tfce.m
M       tfce_estimate_stat.m

(1) Changed: Updated cat_spm_results_ui.m w.r.t. CAT12.
(2) Changed: Removed SPM8 support.
(3) Changed: Added support to use voxel-wise covariates.

------------------------------------------------------------------------
r214 | gaser | 2021-02-05 10:25:58 +0100 (Fri, 05 Feb 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Fixed: Interactive selection with defining contrast as Inf was not working.


------------------------------------------------------------------------
r213 | gaser | 2021-02-05 00:16:01 +0100 (Fri, 05 Feb 2021) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m

Fixed: Calling cat_spm_results_ui from other functions now works correctly.


------------------------------------------------------------------------
r212 | gaser | 2020-12-02 23:58:03 +0100 (Wed, 02 Dec 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Fixed: Check that scl_slope field exist for global scaling of surfaces.


------------------------------------------------------------------------
r211 | gaser | 2020-11-25 17:12:05 +0100 (Wed, 25 Nov 2020) | 16 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html
M       html/tfce_FN.html
A  +    old_tfce_results_ui.m
        > moved from tfce_results_ui.m
D       tfce_results_ui.m
        > moved to old_tfce_results_ui.m

(1) Fixed:   Corrected a typo in html file that called cat_vol_slice_overlay
             (thanks to Do-Joon Yi for pointing to that issue).
(2) Removed: Removed oldtfce_results_ui.m which is not needed anymore because
             now always cat_spm_results_ui.m is used for both CAT12 and TFCE.
(3) Changed: Use updated cat_spm_results_ui.m from CAT12.

------------------------------------------------------------------------
r210 | gaser | 2020-11-24 15:00:29 +0100 (Tue, 24 Nov 2020) | 13 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       spm_TFCE.m
M       tbx_cfg_tfce.m
M       tfceMex_pthread.c
M       tfce_estimate_stat.m

(1) Fixed:   Calculation of multiple SPM.mat files failed if nproc was set to "0".
(2) Changed: Changed data field to support call via cat_standalone.sh.
(3) Changed: Re-implemented option to use old method to estimate maximum 
             statistics from r184 for compatibility purposes.

------------------------------------------------------------------------
r209 | gaser | 2020-09-29 13:59:27 +0200 (Tue, 29 Sep 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Fixed:  Recognition of missing contrasts did not always work.


------------------------------------------------------------------------
r208 | gaser | 2020-09-29 13:00:39 +0200 (Tue, 29 Sep 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       tfce_estimate_stat.m

Fixed:  Always the first contrast was used independent of contrast 
        selection in tfce_estimate_stat.m in r207.

------------------------------------------------------------------------
r207 | gaser | 2020-09-11 11:31:21 +0200 (Fri, 11 Sep 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       html/tfce.html
M       tfce_estimate_stat.m

(1) Changed: Interactive selection of contrasts is not necessary anymore of
             only one contrast is defined.
(2) Changed: Updated Makefile.

------------------------------------------------------------------------
r206 | gaser | 2020-08-19 15:48:12 +0200 (Wed, 19 Aug 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tbx_cfg_tfce.m
M       tfce_estimate_stat.m

Changed: Updated help text.

------------------------------------------------------------------------
r205 | gaser | 2020-08-19 15:30:02 +0200 (Wed, 19 Aug 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       tbx_cfg_tfce.m
M       tfce_estimate_stat.m

(1) Changed: Added option for multiple processes to TFCE.
(2) Changed: Updated Makefile.
(3) Fixed:   Corrected check for validity of design using correlation between 
             parametric and permutation tests for SVC with external mask.

------------------------------------------------------------------------
r204 | gaser | 2020-08-03 14:03:16 +0200 (Mon, 03 Aug 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html
M       tfce_estimate_stat.m

(1) Changed: Updated cat_spm_results_ui.m using newest version from CAT12.
(2) Changed: Added option for using old method for estimating maximum statistic
             from release r184 for compatibility purposes.

------------------------------------------------------------------------
r203 | gaser | 2020-06-23 10:56:50 +0200 (Tue, 23 Jun 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Contents_info.txt
M       cat_spm_results_ui.m
M       html/tfce.html
M       tbx_cfg_tfce.m

(1) Changed: Updated cat_spm_results_ui.m using newest version from CAT12.
(2) Changed: Updated help text.

------------------------------------------------------------------------
r202 | gaser | 2020-05-29 15:14:31 +0200 (Fri, 29 May 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       html/tfce.html
M       tfce_estimate_stat.m

Fixed: Solved issue if covariates across multiple columns were zero.

------------------------------------------------------------------------
r201 | gaser | 2020-04-21 22:38:48 +0200 (Tue, 21 Apr 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cat_spm_results_ui.m
M       html/tfce.html

Fixed: Removed dome inconsitencies in cat_spm_results_ui.m where existing
TFCE results were initially not found. 

------------------------------------------------------------------------
r200 | gaser | 2020-04-20 22:26:23 +0200 (Mon, 20 Apr 2020) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html

Fixed: Removed bug in cat_spm_results_ui.m where surface results could not
be displayed.


------------------------------------------------------------------------
r199 | gaser | 2020-04-13 02:11:38 +0200 (Mon, 13 Apr 2020) | 8 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m
M       html/tfce.html

Fixed: Corrected bug with non-detectable call_list function in 
cat_spm_results_ui.m

------------------------------------------------------------------------
r198 | gaser | 2020-04-13 01:50:47 +0200 (Mon, 13 Apr 2020) | 6 lines

Changed paths:
M       CHANGES.txt
M       tfce_getSPM.m

Fixed: Corrected mesh detection to be compatible to older versions.

------------------------------------------------------------------------
r197 | gaser | 2020-04-13 01:38:21 +0200 (Mon, 13 Apr 2020) | 6 lines

Changed paths:
M       CHANGES.txt
MM      cat_spm_results_ui.m

Fixed: Corrected some inconsistencies in cat_spm_results_ui.m.

------------------------------------------------------------------------
r196 | gaser | 2020-04-10 01:30:56 +0200 (Fri, 10 Apr 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       cat_spm_results_ui.m

Changed: Added check to cat_spm_results_ui if TFCE is installed (for general 
use in CAT12).

------------------------------------------------------------------------
r195 | gaser | 2020-04-10 01:22:07 +0200 (Fri, 10 Apr 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Makefile
A       cat_spm_results_ui.m
M       html/tfce.html
M       spm_TFCE.m
M       tfce_list.m
M       tfce_results_ui.m

(1) Changed: ARenamed tfce_results_ui.m to cat_spm_results_ui.m and added
    functionality from CAT12 result call.
(2) Changed: Corrected internal function names.


------------------------------------------------------------------------
r194 | gaser | 2020-04-09 13:42:16 +0200 (Thu, 09 Apr 2020) | 19 lines

Changed paths:
M       CHANGES.txt
M       Makefile
 M      html/images/TFCE.png
 M      html/images/home.jpg
 M      html/images/research.jpg
 M      html/style.css
MM      html/tfce.html
 M      html/tfce.txt
 M      html/tfce_FN.html
 M      html/tfce_starting.html
M       tfce_estimate_stat.m
M       tfce_results_ui.m

(1) Changed: Added option to list more detailed cluster information in 
    tfce_results_ui.m.
(2) Changed: Corrected internal function name in tfce_estimate_stat.m
(3) Changed: Set server to old dbm-server in Makefile.

------------------------------------------------------------------------
r193 | gaser | 2020-04-09 00:36:57 +0200 (Thu, 09 Apr 2020) | 7 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       html/tfce.html

Changed: Updated Makefile.

------------------------------------------------------------------------
r192 | gaser | 2020-04-09 00:35:26 +0200 (Thu, 09 Apr 2020) | 19 lines

Changed paths:
M       CHANGES.txt
D       TFCE.txt
A       html
A       html/images
A       html/images/TFCE.png
A       html/images/home.jpg
A       html/images/research.jpg
A       html/style.css
A       html/tfce.html
A       html/tfce.txt
A       html/tfce_FN.html
A       html/tfce_starting.html
MM      spm/spm_getSPM.m
MM      spm/spm_list.m
MM      spm/spm_results_ui.m

Added: Added html help text

------------------------------------------------------------------------
r191 | gaser | 2020-04-09 00:33:33 +0200 (Thu, 09 Apr 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       spm_TFCE.m
M       tbx_cfg_tfce.m
M       tfce_list.m
M       tfce_results_ui.m

(1) Changed: Updated Makefile.
(2) Changed: Updated tfce_results_ui.m to implement modifications from 
    cat_stat_spm_results_ui.m for surface visualization of results.
(3) Changed: Implemented function for displaying only current cluster.
(4) Changed: Updated help text.

------------------------------------------------------------------------
r190 | gaser | 2020-04-08 02:26:29 +0200 (Wed, 08 Apr 2020) | 11 lines

Changed paths:
M       CHANGES.txt
M       Makefile
R       spm
A       spm/spm_getSPM.m
A       spm/spm_list.m
A       spm/spm_results_ui.m

(1) Fixed: Resolved conflict with spm folder.
(2) Fixed: Corrected port of ssh command in makefile.

------------------------------------------------------------------------
r189 | gaser | 2020-04-08 02:19:15 +0200 (Wed, 08 Apr 2020) | 87 lines

Changed paths:
M       CHANGES.txt
M       Contents_info.txt
M       INSTALL_info.txt
M       Makefile
M       TFCE.txt
D       cg_get_tfce_results.m
        > moved to tfce_getSPM.m
D       cg_progress.m
        > moved to tfce_progress.m
D       cg_tfce_estimate.m
        > moved to tfce_estimate_stat.m
D       cg_tfce_list.m
        > moved to tfce_list.m
D       cg_tfce_results.m
        > moved to tfce_results_ui.m
D       cg_tfce_surf_max.m
        > moved to tfce_surf_max.m
D       cg_tfce_update.m
        > moved to tfce_update.m
M       compile.m
A  +    old/tfceMex.c
        > moved from tfceMex.c
A  +    old/tfceMex.m
        > moved from tfceMex.m
A  +    old/tfceMex.mexa64
        > moved from tfceMex.mexa64
A  +    old/tfceMex.mexglx
        > moved from tfceMex.mexglx
A  +    old/tfceMex.mexmaci
        > moved from tfceMex.mexmaci
A  +    old/tfceMex.mexmaci64
        > moved from tfceMex.mexmaci64
A  +    old/tfceMex.mexw32
        > moved from tfceMex.mexw32
A  +    old/tfceMex.mexw64
        > moved from tfceMex.mexw64
A       spm
A       spm/spm_getSPM.m
A       spm/spm_list.m
A       spm/spm_results_ui.m
M       spm_TFCE.m
A  +    tbx_cfg_tfce.m
        > moved from tbx_cfg_tfce_estimate.m
D       tbx_cfg_tfce_estimate.m
        > moved to tbx_cfg_tfce.m
D       tfceMex.c
        > moved to old/tfceMex.c
D       tfceMex.m
        > moved to old/tfceMex.m
D       tfceMex.mexa64
        > moved to old/tfceMex.mexa64
D       tfceMex.mexglx
        > moved to old/tfceMex.mexglx
D       tfceMex.mexmaci
        > moved to old/tfceMex.mexmaci
D       tfceMex.mexmaci64
        > moved to old/tfceMex.mexmaci64
D       tfceMex.mexw32
        > moved to old/tfceMex.mexw32
D       tfceMex.mexw64
        > moved to old/tfceMex.mexw64
D       tfceMex_noopenmp.mexa64
D       tfceMex_noopenmp.mexglx
D       tfceMex_noopenmp.mexmaci
D       tfceMex_noopenmp.mexmaci64
D       tfceMex_noopenmp.mexw32
D       tfceMex_noopenmp.mexw64
A  +    tfce_estimate_stat.m
        > moved from cg_tfce_estimate.m
A  +    tfce_getSPM.m
        > moved from cg_get_tfce_results.m
A  +    tfce_list.m
        > moved from cg_tfce_list.m
A  +    tfce_progress.m
        > moved from cg_progress.m
A  +    tfce_results_ui.m
        > moved from cg_tfce_results.m
A  +    tfce_surf_max.m
        > moved from cg_tfce_surf_max.m
A  +    tfce_update.m
        > moved from cg_tfce_update.m

(1) Changed: Renamed all functions to start with "tfce".
(2) Changed: Updated many functions w.r.t. to new functionality in SPM12
    result functions.

------------------------------------------------------------------------
r188 | gaser | 2020-02-25 11:44:14 +0100 (Tue, 25 Feb 2020) | 10 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cg_tfce_estimate.m
M       cg_tfce_update.m

(1) Fixed: Corrected interactive selection of contrasts.
(2) Fixed: Check for empty result masks was not correct.
(3) Changed: IP-address of server changed.

------------------------------------------------------------------------
r187 | gaser | 2020-02-06 16:44:51 +0100 (Thu, 06 Feb 2020) | 14 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       compile.m
M       tfceMex_pthread.mexa64
M       tfceMex_pthread.mexmaci64
M       tfceMex_pthread.mexw64

(1) Fixed: F-test for some contrasts was not correct and ended up with 
    discrepancy between parametric and non-parametric statistic.
(2) Fixed: Corrected interactive selection of contrasts.
(3) Fixed: Check for empty result masks was not correct.
(4) Changed: Updated compiler flags and recompiled tfceMex_pthread.c

------------------------------------------------------------------------
r186 | gaser | 2019-12-03 10:46:25 +0100 (Tue, 03 Dec 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

(1) Fixed: Tail approximation was not correct for estimating inverse contrasts.
    Any other (defined) contrasts were not affected.
(2) Fixed: Design check for interaction designs is now correctly printed.

------------------------------------------------------------------------
r185 | gaser | 2019-11-18 12:01:39 +0100 (Mon, 18 Nov 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tfceMex_pthread.mexmaci64

(1) Fixed: Check computation time between multi-threading cto identify 
    potential issues with multi-threading on some systems (it is not clear where
    these longer computation time by a factor of > 10 time come from).
(2) Changed: Maximum statistic is now using a different mask.

------------------------------------------------------------------------
r184 | gaser | 2019-09-19 23:48:18 +0200 (Thu, 19 Sep 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       tbx_cfg_tfce_estimate.m

Changed: Updated help text.

------------------------------------------------------------------------
r183 | gaser | 2019-08-14 13:07:22 +0200 (Wed, 14 Aug 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Changed criteria for checking discrepancy between parametric and 
non-parametric statistic w.r.t. use of SVC.

------------------------------------------------------------------------
r182 | gaser | 2019-08-09 17:02:06 +0200 (Fri, 09 Aug 2019) | 9 lines

Changed paths:
M       CHANGES.txt
M       tfceMex_pthread.c
M       tfceMex_pthread.mexa64
M       tfceMex_pthread.mexmaci64
M       tfceMex_pthread.mexw64

Changed: Improved speed of tfceMex_pthread by still being thread-safe.

------------------------------------------------------------------------
r181 | gaser | 2019-05-17 09:22:47 +0200 (Fri, 17 May 2019) | 11 lines

Changed paths:
M       CHANGES.txt
M       TFCE.txt
M       cg_tfce_estimate.m
M       tfceMex_pthread.c
M       tfceMex_pthread.mexmaci64

(1) Fixed: Tail approximation for inverse contrast was not correct.
(2) Fixed: tfceMex_pthread is now thread-safe and the same results are obtained
    independent from number of threads or without multi-threading.

------------------------------------------------------------------------
r180 | gaser | 2019-05-09 11:55:13 +0200 (Thu, 09 May 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Some cosmetic changes to cg_tfce_estimate.m

------------------------------------------------------------------------
r179 | gaser | 2019-05-08 17:40:34 +0200 (Wed, 08 May 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Speeded up GLM calculation by up to 50%!

------------------------------------------------------------------------
r178 | gaser | 2019-05-08 11:25:14 +0200 (Wed, 08 May 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Added tail approximation from Gamma distribution for corrected P-values.

------------------------------------------------------------------------
r177 | gaser | 2019-04-16 04:35:06 +0200 (Tue, 16 Apr 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       Contents_info.txt
M       TFCE.txt

Changed: Added new version information.

------------------------------------------------------------------------
r176 | gaser | 2019-04-16 04:32:02 +0200 (Tue, 16 Apr 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       spm_TFCE.m

Changed: Added new version information.

------------------------------------------------------------------------
r175 | gaser | 2019-04-12 02:22:34 +0200 (Fri, 12 Apr 2019) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected bug that occurred if no effects could be found for that design
(thanks to Larry Lai for pinting to that).

------------------------------------------------------------------------
r174 | gaser | 2019-01-07 13:01:44 +0100 (Mon, 07 Jan 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected detection of multiple regression with F-contrasts.

------------------------------------------------------------------------
r173 | gaser | 2019-01-07 12:58:05 +0100 (Mon, 07 Jan 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected detection of multiple regression with F-contrasts.

------------------------------------------------------------------------
r172 | gaser | 2019-01-07 01:52:47 +0100 (Mon, 07 Jan 2019) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected bug for non-estimated contrasts.

------------------------------------------------------------------------
r171 | gaser | 2019-01-03 16:12:22 +0100 (Thu, 03 Jan 2019) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

(1) Fixed: xCon was not correctly set for multiple contrasts.
(2) Changed: Added output for checking correlation between between parametric 
    and non-parametric T statistic.

------------------------------------------------------------------------
r170 | gaser | 2019-01-02 23:58:22 +0100 (Wed, 02 Jan 2019) | 10 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

(1) Fixed: Corrected bug if multiple contrasts were used in batch mode.
(2) Changed: Whitening matrix is not permuted anymore because of unreliable
    results.
(3) Changed: Calculation of F-test is not using spm_FcUtils anymore because
    of unreliable results.

------------------------------------------------------------------------
r169 | gaser | 2018-12-28 15:58:03 +0100 (Fri, 28 Dec 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected check for a low correlation between parametric and non-parametric 
p-values.


------------------------------------------------------------------------
r168 | gaser | 2018-12-20 17:36:17 +0100 (Thu, 20 Dec 2018) | 10 lines

Changed paths:
M       CHANGES.txt
M       Makefile
M       cg_tfce_estimate.m

(1) Changed: Added check for a low correlation between parametric and 
    non-parametric p-values.
(2) Changed: Added experimental option for bilateral filtering (which almost
    has no effect).

------------------------------------------------------------------------
r167 | gaser | 2018-09-26 16:12:23 +0200 (Wed, 26 Sep 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Chaned: Added some more support for F-contrasts.

------------------------------------------------------------------------
r166 | gaser | 2018-09-25 16:17:14 +0200 (Tue, 25 Sep 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Regression design where contrast is defined for covariate is now 
handled correctly?

------------------------------------------------------------------------
r165 | gaser | 2018-09-20 09:29:24 +0200 (Thu, 20 Sep 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: For comparisons between groups with equal number of subjects the plot
was not displayed.

------------------------------------------------------------------------
r164 | gaser | 2018-06-05 14:10:32 +0200 (Tue, 05 Jun 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: FDisabled F-tests in cg_tfce_estimate.m because of potential errors
with some contrasts.

------------------------------------------------------------------------
r163 | gaser | 2018-05-28 23:32:57 +0200 (Mon, 28 May 2018) | 7 lines

Changed paths:
M       CHANGES.txt
 M      SPM-Designs-Permutation.rtf
M       cg_tfce_estimate.m

Fixed: Don't allow F-contrasts with multiple rows currently...

------------------------------------------------------------------------
r162 | gaser | 2018-05-27 17:56:16 +0200 (Sun, 27 May 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

(1) Fixed: Some sparse contrasts in complex designs were not correctly
    supported in cg_tfce_estimate.m.
(2) Changed: Updated and renamed SPM-Designs-Permutation.rtf

------------------------------------------------------------------------
r161 | gaser | 2018-05-27 17:54:23 +0200 (Sun, 27 May 2018) | 10 lines

Changed paths:
M       CHANGES.txt
D       SPM-Designs-Permutation.doc
A       SPM-Designs-Permutation.rtf
M       cg_tfce_estimate.m

(1) Fixed: Some sparse contrasts in complex designs were not correctly
    supported in cg_tfce_estimate.m.
(2) Changed: Updated and renamed SPM-Designs-Permutation.rtf

------------------------------------------------------------------------
r160 | gaser | 2018-05-14 11:01:44 +0200 (Mon, 14 May 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Fixed some smaller issues with on-sample t-test in cg_tfce_estimate.m

------------------------------------------------------------------------
r159 | gaser | 2018-05-11 23:43:54 +0200 (Fri, 11 May 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected bug in cg_tfce_estimate.m for one-sample t-test (thanks
to Larry Lai for pointing to this bug).

------------------------------------------------------------------------
r158 | gaser | 2018-05-07 10:11:41 +0200 (Mon, 07 May 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Forgot to remove debugging code in cg_tfce_estimate.m

------------------------------------------------------------------------
r157 | gaser | 2018-05-07 00:02:12 +0200 (Mon, 07 May 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Some very rare designs were not working where in an interaction
design the covariate was not defined for all data.

------------------------------------------------------------------------
r156 | gaser | 2018-04-23 10:21:09 +0200 (Mon, 23 Apr 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Set some parameters for plotting back to r153 because on some 
computers processes stalled.

------------------------------------------------------------------------
r155 | gaser | 2018-04-09 15:55:37 +0200 (Mon, 09 Apr 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       TFCE.txt

Changed: Updated version information.

------------------------------------------------------------------------
r154 | gaser | 2018-03-14 16:13:38 +0100 (Wed, 14 Mar 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected missing graphical output for designs with equal number of 
subjects.

------------------------------------------------------------------------
r153 | gaser | 2018-02-18 23:15:57 +0100 (Sun, 18 Feb 2018) | 12 lines

Changed paths:
M       CHANGES.txt
M       Makefile
D       cat_surf_max.m
        > moved to cg_tfce_surf_max.m
M       cg_tfce_list.m
A  +    cg_tfce_surf_max.m
        > moved from cat_surf_max.m

Changed: Renamed cat_surf_max.m to cg_tfce_surf_max.m to not interfere
with older versions of the same function in CAT12.

------------------------------------------------------------------------
r152 | gaser | 2018-02-18 23:04:05 +0100 (Sun, 18 Feb 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cat_surf_max.m

Fixed: In rare cases where local maxima are not correctly found the 
number of clusters differs from cluster indices in A. Then, we have 
to add non-unique entries using function find_connected_component
in cat_surf_max.m.

------------------------------------------------------------------------
r151 | gaser | 2018-02-16 16:01:14 +0100 (Fri, 16 Feb 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Filenames for GUI-selected contrasts were not correct.

------------------------------------------------------------------------
r150 | gaser | 2018-02-16 00:13:38 +0100 (Fri, 16 Feb 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Now non-differential F-contrasts really work in cg_tfce_estimate.m.


------------------------------------------------------------------------
r149 | gaser | 2018-02-15 22:09:31 +0100 (Thu, 15 Feb 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Removed debugging output in cg_tfce_estimate.m.

------------------------------------------------------------------------
r148 | gaser | 2018-02-15 22:06:24 +0100 (Thu, 15 Feb 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Sometimes the rank of xKXs in cg_tfce_estimate.m is not correct
and spm_FcUtil('Hsqr',xCon,xKXs) is not working.

------------------------------------------------------------------------
r147 | gaser | 2018-02-15 22:05:41 +0100 (Thu, 15 Feb 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Sometimes the rank of xKXs in cg_tfce_estimate.m is not correct
and spm_FcUtil('Hsqr',xCon,xKXs) is not working.

------------------------------------------------------------------------
r146 | gaser | 2018-02-15 21:30:39 +0100 (Thu, 15 Feb 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Non-differential F-contrast were not working in cg_tfce_estimate.m.


------------------------------------------------------------------------
r145 | gaser | 2018-02-14 17:44:32 +0100 (Wed, 14 Feb 2018) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Updated some graphical output in cg_tfce_estimate.m

------------------------------------------------------------------------
r144 | gaser | 2018-02-14 09:11:08 +0100 (Wed, 14 Feb 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Added again variance smoothing for volumes to cg_tfce_estimate.m
(experimental).

------------------------------------------------------------------------
r143 | gaser | 2018-02-13 08:42:40 +0100 (Tue, 13 Feb 2018) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Check for rng-function was not correct (builtin-flag is necessary) in
cg_tfce_estimate.m

------------------------------------------------------------------------
r142 | gaser | 2018-02-12 22:34:39 +0100 (Mon, 12 Feb 2018) | 8 lines

Changed paths:
M       CHANGES.txt
M       SPM-Designs-Permutation.doc
M       cg_tfce_estimate.m

(1) Changed: Updated global scaling in cg_tfce_estimate.m
(2) Changed: Updated table in SPM-Designs-Permutation.doc.

------------------------------------------------------------------------
r141 | gaser | 2018-01-15 08:46:22 +0100 (Mon, 15 Jan 2018) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

(1) Changed: Force use of -v7.3 option to save SPM.mat in cg_tfce_estimate.m
(2) Changed: Removed check whether iB (subject effects) should be larger than 
    iH (time effects), because this was not always working in cg_tfce_estimate.m

------------------------------------------------------------------------
r140 | gaser | 2017-12-01 00:08:53 +0100 (Fri, 01 Dec 2017) | 9 lines

Changed paths:
M       CHANGES.txt
MM      cat_surf_max.m
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

Changed: Added Smith permutation method as default to deal with nuisance
parameters.

------------------------------------------------------------------------
r139 | gaser | 2017-11-30 15:57:39 +0100 (Thu, 30 Nov 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       tbx_cfg_tfce_estimate.m

Changed: Removed option for automatically selecting Freedman-Lane or Draper-Stoneman
correction because Freedman-lane seems to deviate results depending on a potential
correlation of your nuisance parameter(s) and your effects of interest.


------------------------------------------------------------------------
r138 | gaser | 2017-11-06 21:18:00 +0100 (Mon, 06 Nov 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_get_tfce_results.m

Changed: If underlying mesh saved in SPM.xVol.G is not found a mesh with the
same name in the toolbox/cat12/templates_surfaces folder is used.

------------------------------------------------------------------------
r137 | gaser | 2017-11-06 17:08:08 +0100 (Mon, 06 Nov 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       Makefile
A       cat_surf_max.m
M       cg_tfce_list.m

(1) Added: cat_surf_max.m as modified version of spm_mesh_max because for some 
    rare data only one global maximum was returned.
(2) Changed: Replaced spm_mesh_max by cat_surf_max in cg_tfce_list.m.

------------------------------------------------------------------------
r136 | gaser | 2017-10-19 11:12:23 +0200 (Thu, 19 Oct 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: If only one constant factors such as mean is used in the design this
is now correctly detected for choosing method to deal with nuisance parameters.

------------------------------------------------------------------------
r135 | gaser | 2017-09-08 16:03:15 +0200 (Fri, 08 Sep 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       svn_ci_log

Changed: Updated svn log system

------------------------------------------------------------------------
r134 | gaser | 2017-09-08 15:38:03 +0200 (Fri, 08 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       tfceMex_pthread.mexw64

Changed: Recompiled Windows mex-files with pthread.


------------------------------------------------------------------------
r133 | gaser | 2017-09-07 10:33:16 +0200 (Thu, 07 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected error in cg_tfce_estimate for progress status.


------------------------------------------------------------------------
r132 | gaser | 2017-09-07 10:29:59 +0200 (Thu, 07 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Updated code for initialization in cg_tfce_estimate.


------------------------------------------------------------------------
r131 | gaser | 2017-09-07 10:24:01 +0200 (Thu, 07 Sep 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Corrected ismember error for newer matlab versions in cg_tfce_estimate.

------------------------------------------------------------------------
r130 | gaser | 2017-09-07 09:47:37 +0200 (Thu, 07 Sep 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       TFCE.txt
M       cg_tfce_update.m
M       tfceMex_pthread.mexa64

Changed: Updated intro text and update function.

------------------------------------------------------------------------
r129 | gaser | 2017-09-06 12:52:18 +0200 (Wed, 06 Sep 2017) | 14 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       compile.m
M       tbx_cfg_tfce_estimate.m
M       tfceMex_pthread.c
M       tfceMex_pthread.mexmaci64

(1) Changed: Recompiled mex-files using Matlab R2017a for Mac because of
compatibility issues.
(2) Fixed: Wrong data type for dims parameter in mex-files.
(3) Added: Larger weighting for broader clusters can be now selected in 
the GUI.

------------------------------------------------------------------------
r128 | gaser | 2017-09-03 11:48:25 +0200 (Sun, 03 Sep 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Automatic detection of test-mode in cg_tfce_estimate.m was not
working correctly.

------------------------------------------------------------------------
r127 | gaser | 2017-09-03 00:22:12 +0200 (Sun, 03 Sep 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Added again test mode for checking designs without data.

------------------------------------------------------------------------
r126 | gaser | 2017-08-24 00:05:53 +0200 (Thu, 24 Aug 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

(1) Changed: Added automatic mode for selection of best nuisance method.
(2) Changed: Removed test-mode in cg_tfce_estimate.m.

------------------------------------------------------------------------
r125 | gaser | 2017-08-23 16:59:44 +0200 (Wed, 23 Aug 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tfceMex_pthread.m
M       tfce_mesh.m

(1) Changed: Added some help text.
(2) Changed: Added TFCE parameters E and H to tfce_mesh.m function.

------------------------------------------------------------------------
r124 | gaser | 2017-08-23 14:21:20 +0200 (Wed, 23 Aug 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Some formatting.

------------------------------------------------------------------------
r123 | gaser | 2017-08-13 17:38:33 +0200 (Sun, 13 Aug 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       tfce_mesh.m

Fixed: Removed peak error in tfce_mesh.m

------------------------------------------------------------------------
r122 | gaser | 2017-08-11 22:48:09 +0200 (Fri, 11 Aug 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       TFCE.txt
M       tbx_cfg_tfce_estimate.m
M       tfce_mesh.m

(1) Changed: Saved computation time for meshes by 50%!
(2) Changed: Use Draper-Stoneman correction for nuisance variables as
    default.

------------------------------------------------------------------------
r121 | gaser | 2017-06-20 17:03:38 +0200 (Tue, 20 Jun 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Check for interaction design in r120 was not correct.

------------------------------------------------------------------------
r120 | gaser | 2017-06-20 16:28:46 +0200 (Tue, 20 Jun 2017) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

Fixed: Complex interaction designs are now fully considered.

------------------------------------------------------------------------
r119 | gaser | 2017-04-06 22:04:46 +0200 (Thu, 06 Apr 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Global scaling was not working.

------------------------------------------------------------------------
r118 | gaser | 2017-04-06 08:52:30 +0200 (Thu, 06 Apr 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       cg_tfce_update.m

Fixed: Reduced designs where not all data are covered by the contrast
       are now working.


------------------------------------------------------------------------
r117 | gaser | 2017-03-30 14:41:31 +0200 (Thu, 30 Mar 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       tbx_cfg_tfce_estimate.m

Changed: Use Draper-Stoneman permutation as default.

------------------------------------------------------------------------
r116 | gaser | 2017-03-30 14:40:00 +0200 (Thu, 30 Mar 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Deselected z-transformation by default.

------------------------------------------------------------------------
r115 | gaser | 2017-03-29 13:34:38 +0200 (Wed, 29 Mar 2017) | 10 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

(1) Changed: If no mask file is found then test mode is automatically selected.
(2) Fixed: Prevent neg. values for F-test after z-transformation.
(3) Fixed: Prevent Nan and Inf values after z-transformation.
(4) Fixed: Incorrect permutations for repeated measurement ANOVAs

------------------------------------------------------------------------
r114 | gaser | 2017-03-27 00:17:26 +0200 (Mon, 27 Mar 2017) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

(1) Changed: Added choice of permutation method to the GUI.
(2) Fixed: Corrected Freeman-Lane permutation where Pset was not transposed.

------------------------------------------------------------------------
r113 | gaser | 2017-03-24 20:08:00 +0100 (Fri, 24 Mar 2017) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       cg_tfce_results.m

(1) Changed: Completely reorganized and recoded permutation with some ideas from 
    palm
(2) Changed: Added z-transformation and Freeman-Lane shuffling

------------------------------------------------------------------------
r112 | gaser | 2017-02-17 11:44:01 +0100 (Fri, 17 Feb 2017) | 13 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

(1) Added: Conversion to z-statistics according to palm which makes TFCE
    distribution more reliable for very small datasets.
(2) Changed: 3D data are now read with nifti strauture which is much more 
    faster.
(3) Changed: Estimation of uncorrected thresholds is not using cummulated
    histogram.
(4) Changed: Shared function for estimating GLM for F- and T-statistics.
(5) Added: Palm function for F-to-z transformation are now added.

------------------------------------------------------------------------
r111 | gaser | 2017-01-25 19:35:39 +0100 (Wed, 25 Jan 2017) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Check for contrasts for columns with subject effects in repeated anovas.

------------------------------------------------------------------------
r110 | gaser | 2016-11-11 16:58:05 +0100 (Fri, 11 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Forgot to define W in cg_tfce_estimate.m


------------------------------------------------------------------------
r109 | gaser | 2016-11-11 16:40:53 +0100 (Fri, 11 Nov 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: Whitening of design matrix is changed (although still not sure
about the permutation of the whitening matrix).

------------------------------------------------------------------------
r108 | gaser | 2016-11-11 11:40:26 +0100 (Fri, 11 Nov 2016) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_progress.m
M       cg_tfce_estimate.m
M       cg_tfce_results.m

Changed: Added IDs and some help text to functions.

------------------------------------------------------------------------
r107 | gaser | 2016-11-09 08:09:04 +0100 (Wed, 09 Nov 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Changed: rand initialization is now using "twister".

------------------------------------------------------------------------
r106 | gaser | 2016-11-08 14:49:07 +0100 (Tue, 08 Nov 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Interaction contrasts were not correctly accepted.

------------------------------------------------------------------------
r105 | gaser | 2016-11-03 14:41:00 +0100 (Thu, 03 Nov 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

Fixed: Exchangeability blocks were redundant for interaction designs.

------------------------------------------------------------------------
r104 | gaser | 2016-09-22 16:12:12 +0200 (Thu, 22 Sep 2016) | 8 lines

Changed paths:
M       CHANGES.txt
D       branches
D       tag
D       trunk

Changed: Moved back from trunk...

------------------------------------------------------------------------
r103 | gaser | 2016-09-22 16:10:38 +0200 (Thu, 22 Sep 2016) | 224 lines

Changed paths:
A  +    CHANGES.txt
        > moved from trunk/CHANGES.txt
A  +    Contents_info.txt
        > moved from trunk/Contents_info.txt
A  +    INSTALL_info.txt
        > moved from trunk/INSTALL_info.txt
A  +    Makefile
        > moved from trunk/Makefile
A  +    SPM-Designs-Permutation.doc
        > moved from trunk/SPM-Designs-Permutation.doc
A  +    TFCE.txt
        > moved from trunk/TFCE.txt
A  +    cg_get_tfce_results.m
        > moved from trunk/cg_get_tfce_results.m
A  +    cg_progress.m
        > moved from trunk/cg_progress.m
A  +    cg_tfce_estimate.m
        > moved from trunk/cg_tfce_estimate.m
A  +    cg_tfce_list.m
        > moved from trunk/cg_tfce_list.m
A  +    cg_tfce_results.m
        > moved from trunk/cg_tfce_results.m
A  +    cg_tfce_update.m
        > moved from trunk/cg_tfce_update.m
A  +    compile.m
        > moved from trunk/compile.m
A  +    old
        > moved from trunk/old
A  +    questions.txt
        > moved from trunk/questions.txt
A  +    snpm_P_FDR.m
        > moved from trunk/snpm_P_FDR.m
A  +    spm_TFCE.m
        > moved from trunk/spm_TFCE.m
A  +    svn_ci_log
        > moved from trunk/svn_ci_log
A  +    tbx_cfg_tfce_estimate.m
        > moved from trunk/tbx_cfg_tfce_estimate.m
A  +    tfceMex.c
        > moved from trunk/tfceMex.c
A  +    tfceMex.m
        > moved from trunk/tfceMex.m
A  +    tfceMex.mexa64
        > moved from trunk/tfceMex.mexa64
A  +    tfceMex.mexglx
        > moved from trunk/tfceMex.mexglx
A  +    tfceMex.mexmaci
        > moved from trunk/tfceMex.mexmaci
A  +    tfceMex.mexmaci64
        > moved from trunk/tfceMex.mexmaci64
A  +    tfceMex.mexw32
        > moved from trunk/tfceMex.mexw32
A  +    tfceMex.mexw64
        > moved from trunk/tfceMex.mexw64
A  +    tfceMex_noopenmp.mexa64
        > moved from trunk/tfceMex_noopenmp.mexa64
A  +    tfceMex_noopenmp.mexglx
        > moved from trunk/tfceMex_noopenmp.mexglx
A  +    tfceMex_noopenmp.mexmaci
        > moved from trunk/tfceMex_noopenmp.mexmaci
A  +    tfceMex_noopenmp.mexmaci64
        > moved from trunk/tfceMex_noopenmp.mexmaci64
A  +    tfceMex_noopenmp.mexw32
        > moved from trunk/tfceMex_noopenmp.mexw32
A  +    tfceMex_noopenmp.mexw64
        > moved from trunk/tfceMex_noopenmp.mexw64
A  +    tfceMex_pthread.c
        > moved from trunk/tfceMex_pthread.c
A  +    tfceMex_pthread.m
        > moved from trunk/tfceMex_pthread.m
A  +    tfceMex_pthread.mexa64
        > moved from trunk/tfceMex_pthread.mexa64
A  +    tfceMex_pthread.mexmaci64
        > moved from trunk/tfceMex_pthread.mexmaci64
A  +    tfceMex_pthread.mexw64
        > moved from trunk/tfceMex_pthread.mexw64
A  +    tfce_mesh.m
        > moved from trunk/tfce_mesh.m
A  +    todo
        > moved from trunk/todo
D       trunk/CHANGES.txt
        > moved to CHANGES.txt
D       trunk/Contents_info.txt
        > moved to Contents_info.txt
D       trunk/INSTALL_info.txt
        > moved to INSTALL_info.txt
D       trunk/Makefile
        > moved to Makefile
D       trunk/SPM-Designs-Permutation.doc
        > moved to SPM-Designs-Permutation.doc
D       trunk/TFCE.txt
        > moved to TFCE.txt
D       trunk/cg_get_tfce_results.m
        > moved to cg_get_tfce_results.m
D       trunk/cg_progress.m
        > moved to cg_progress.m
D       trunk/cg_tfce_estimate.m
        > moved to cg_tfce_estimate.m
D       trunk/cg_tfce_list.m
        > moved to cg_tfce_list.m
D       trunk/cg_tfce_results.m
        > moved to cg_tfce_results.m
D       trunk/cg_tfce_update.m
        > moved to cg_tfce_update.m
D       trunk/compile.m
        > moved to compile.m
D       trunk/old
        > moved to old
D       trunk/old/cg_glm_get_Beta_ResSS.c
D       trunk/old/cg_glm_get_Beta_ResSS.m
D       trunk/old/cg_glm_get_Beta_ResSS.mexa64
D       trunk/old/cg_glm_get_Beta_ResSS.mexglx
D       trunk/old/cg_glm_get_Beta_ResSS.mexmaci
D       trunk/old/cg_glm_get_Beta_ResSS.mexmaci64
D       trunk/old/cg_glm_get_Beta_ResSS.mexw32
D       trunk/old/cg_glm_get_Beta_ResSS.mexw64
D       trunk/old/cg_glm_get_Beta_ResSS_noopenmp.mexa64
D       trunk/old/cg_glm_get_Beta_ResSS_noopenmp.mexglx
D       trunk/old/cg_glm_get_Beta_ResSS_noopenmp.mexmaci
D       trunk/old/cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
D       trunk/old/cg_glm_get_Beta_ResSS_noopenmp.mexw32
D       trunk/old/cg_glm_get_Beta_ResSS_noopenmp.mexw64
D       trunk/old/spm_datatypes.h
D       trunk/old/spm_getdata.c
D       trunk/old/spm_getdata.h
D       trunk/old/spm_getdata.mexw32.obj
D       trunk/old/spm_getdata.mexw64.obj
D       trunk/old/spm_make_lookup.c
D       trunk/old/spm_make_lookup.h
D       trunk/old/spm_make_lookup.mexw32.obj
D       trunk/old/spm_make_lookup.mexw64.obj
D       trunk/old/spm_mapping.c
D       trunk/old/spm_mapping.h
D       trunk/old/spm_mapping.mexw32.obj
D       trunk/old/spm_mapping.mexw64.obj
D       trunk/old/spm_vol_access.c
D       trunk/old/spm_vol_access.h
D       trunk/old/spm_vol_access.mexw32.obj
D       trunk/old/spm_vol_access.mexw64.obj
D       trunk/old/spm_vol_utils.c
D       trunk/old/utils_double.mexw32.obj
D       trunk/old/utils_double.mexw64.obj
D       trunk/old/utils_double_s.mexw32.obj
D       trunk/old/utils_double_s.mexw64.obj
D       trunk/old/utils_float.mexw32.obj
D       trunk/old/utils_float.mexw64.obj
D       trunk/old/utils_float_s.mexw32.obj
D       trunk/old/utils_float_s.mexw64.obj
D       trunk/old/utils_int.mexw32.obj
D       trunk/old/utils_int.mexw64.obj
D       trunk/old/utils_int_s.mexw32.obj
D       trunk/old/utils_int_s.mexw64.obj
D       trunk/old/utils_schar.mexw32.obj
D       trunk/old/utils_schar.mexw64.obj
D       trunk/old/utils_short.mexw32.obj
D       trunk/old/utils_short.mexw64.obj
D       trunk/old/utils_short_s.mexw32.obj
D       trunk/old/utils_short_s.mexw64.obj
D       trunk/old/utils_uchar.mexw32.obj
D       trunk/old/utils_uchar.mexw64.obj
D       trunk/old/utils_uint.mexw32.obj
D       trunk/old/utils_uint.mexw64.obj
D       trunk/old/utils_uint_s.mexw32.obj
D       trunk/old/utils_uint_s.mexw64.obj
D       trunk/old/utils_ushort.mexw32.obj
D       trunk/old/utils_ushort.mexw64.obj
D       trunk/old/utils_ushort_s.mexw32.obj
D       trunk/old/utils_ushort_s.mexw64.obj
D       trunk/questions.txt
        > moved to questions.txt
D       trunk/snpm_P_FDR.m
        > moved to snpm_P_FDR.m
D       trunk/spm_TFCE.m
        > moved to spm_TFCE.m
D       trunk/svn_ci_log
        > moved to svn_ci_log
D       trunk/tbx_cfg_tfce_estimate.m
        > moved to tbx_cfg_tfce_estimate.m
D       trunk/tfceMex.c
        > moved to tfceMex.c
D       trunk/tfceMex.m
        > moved to tfceMex.m
D       trunk/tfceMex.mexa64
        > moved to tfceMex.mexa64
D       trunk/tfceMex.mexglx
        > moved to tfceMex.mexglx
D       trunk/tfceMex.mexmaci
        > moved to tfceMex.mexmaci
D       trunk/tfceMex.mexmaci64
        > moved to tfceMex.mexmaci64
D       trunk/tfceMex.mexw32
        > moved to tfceMex.mexw32
D       trunk/tfceMex.mexw64
        > moved to tfceMex.mexw64
D       trunk/tfceMex_noopenmp.mexa64
        > moved to tfceMex_noopenmp.mexa64
D       trunk/tfceMex_noopenmp.mexglx
        > moved to tfceMex_noopenmp.mexglx
D       trunk/tfceMex_noopenmp.mexmaci
        > moved to tfceMex_noopenmp.mexmaci
D       trunk/tfceMex_noopenmp.mexmaci64
        > moved to tfceMex_noopenmp.mexmaci64
D       trunk/tfceMex_noopenmp.mexw32
        > moved to tfceMex_noopenmp.mexw32
D       trunk/tfceMex_noopenmp.mexw64
        > moved to tfceMex_noopenmp.mexw64
D       trunk/tfceMex_pthread.c
        > moved to tfceMex_pthread.c
D       trunk/tfceMex_pthread.m
        > moved to tfceMex_pthread.m
D       trunk/tfceMex_pthread.mexa64
        > moved to tfceMex_pthread.mexa64
D       trunk/tfceMex_pthread.mexmaci64
        > moved to tfceMex_pthread.mexmaci64
D       trunk/tfceMex_pthread.mexw64
        > moved to tfceMex_pthread.mexw64
D       trunk/tfce_mesh.m
        > moved to tfce_mesh.m
D       trunk/todo
        > moved to todo

Changed: Moved back from trunk...

------------------------------------------------------------------------
r102 | gaser | 2016-09-22 15:23:39 +0200 (Thu, 22 Sep 2016) | 10 lines

Changed paths:
D       branch
        > moved to branches
A  +    branches
        > moved from branch
M       trunk/CHANGES.txt

Fixed: Corrected branch name.


------------------------------------------------------------------------
r101 | gaser | 2016-09-22 03:22:18 +0200 (Thu, 22 Sep 2016) | 10 lines

Changed paths:
A  +    branch
        > moved from branches
D       branches
        > moved to branch
M       trunk/CHANGES.txt

Fixed: Corrected branch name.


------------------------------------------------------------------------
r100 | gaser | 2016-09-22 03:18:31 +0200 (Thu, 22 Sep 2016) | 7 lines

Changed paths:
M       trunk/CHANGES.txt
M       trunk/svn_ci_log

Fixed: Corrected svn_ci_log to work with subfolders.


------------------------------------------------------------------------
r99 | gaser | 2016-09-22 03:17:20 +0200 (Thu, 22 Sep 2016) | 7 lines

Changed paths:
M       trunk/CHANGES.txt
M       trunk/svn_ci_log

Fixed: Corrected svn_ci_log to work with subfolders.


------------------------------------------------------------------------
r98 | gaser | 2016-09-22 03:16:58 +0200 (Thu, 22 Sep 2016) | 44 lines

Changed paths:
M       trunk/CHANGES.txt
 M      trunk/INSTALL_info.txt
 M      trunk/old/spm_getdata.mexw32.obj
 M      trunk/old/spm_getdata.mexw64.obj
 M      trunk/old/spm_make_lookup.mexw32.obj
 M      trunk/old/spm_make_lookup.mexw64.obj
 M      trunk/old/spm_mapping.mexw32.obj
 M      trunk/old/spm_mapping.mexw64.obj
 M      trunk/old/spm_vol_access.mexw32.obj
 M      trunk/old/spm_vol_access.mexw64.obj
 M      trunk/old/utils_double.mexw32.obj
 M      trunk/old/utils_double.mexw64.obj
 M      trunk/old/utils_double_s.mexw32.obj
 M      trunk/old/utils_double_s.mexw64.obj
 M      trunk/old/utils_float.mexw32.obj
 M      trunk/old/utils_float.mexw64.obj
 M      trunk/old/utils_float_s.mexw32.obj
 M      trunk/old/utils_float_s.mexw64.obj
 M      trunk/old/utils_int.mexw32.obj
 M      trunk/old/utils_int.mexw64.obj
 M      trunk/old/utils_int_s.mexw32.obj
 M      trunk/old/utils_int_s.mexw64.obj
 M      trunk/old/utils_schar.mexw32.obj
 M      trunk/old/utils_schar.mexw64.obj
 M      trunk/old/utils_short.mexw32.obj
 M      trunk/old/utils_short.mexw64.obj
 M      trunk/old/utils_short_s.mexw32.obj
 M      trunk/old/utils_short_s.mexw64.obj
 M      trunk/old/utils_uchar.mexw32.obj
 M      trunk/old/utils_uchar.mexw64.obj
 M      trunk/old/utils_uint.mexw32.obj
 M      trunk/old/utils_uint.mexw64.obj
 M      trunk/old/utils_uint_s.mexw32.obj
 M      trunk/old/utils_uint_s.mexw64.obj
 M      trunk/old/utils_ushort.mexw32.obj
 M      trunk/old/utils_ushort.mexw64.obj
 M      trunk/old/utils_ushort_s.mexw32.obj
 M      trunk/old/utils_ushort_s.mexw64.obj
M       trunk/svn_ci_log

Fixed: Corrected svn_ci_log to work with subfolders.


------------------------------------------------------------------------
r97 | gaser | 2016-09-22 03:15:03 +0200 (Thu, 22 Sep 2016) | 6 lines

Changed paths:
M       trunk/CHANGES.txt
M       trunk/svn_ci_log

Fixed: Corrected svn_ci_log to work with subfolders.

------------------------------------------------------------------------
r96 | gaser | 2016-09-22 03:14:18 +0200 (Thu, 22 Sep 2016) | 227 lines

Changed paths:
D       CHANGES.txt
        > moved to trunk/CHANGES.txt
D       Contents_info.txt
        > moved to trunk/Contents_info.txt
D       INSTALL_info.txt
        > moved to trunk/INSTALL_info.txt
D       Makefile
        > moved to trunk/Makefile
D       SPM-Designs-Permutation.doc
        > moved to trunk/SPM-Designs-Permutation.doc
D       TFCE.txt
        > moved to trunk/TFCE.txt
A       branches
D       cg_get_tfce_results.m
        > moved to trunk/cg_get_tfce_results.m
D       cg_progress.m
        > moved to trunk/cg_progress.m
D       cg_tfce_estimate.m
        > moved to trunk/cg_tfce_estimate.m
D       cg_tfce_list.m
        > moved to trunk/cg_tfce_list.m
D       cg_tfce_results.m
        > moved to trunk/cg_tfce_results.m
D       cg_tfce_update.m
        > moved to trunk/cg_tfce_update.m
D       compile.m
        > moved to trunk/compile.m
D       old
        > moved to trunk/old
D       old/cg_glm_get_Beta_ResSS.c
D       old/cg_glm_get_Beta_ResSS.m
D       old/cg_glm_get_Beta_ResSS.mexa64
D       old/cg_glm_get_Beta_ResSS.mexglx
D       old/cg_glm_get_Beta_ResSS.mexmaci
D       old/cg_glm_get_Beta_ResSS.mexmaci64
D       old/cg_glm_get_Beta_ResSS.mexw32
D       old/cg_glm_get_Beta_ResSS.mexw64
D       old/cg_glm_get_Beta_ResSS_noopenmp.mexa64
D       old/cg_glm_get_Beta_ResSS_noopenmp.mexglx
D       old/cg_glm_get_Beta_ResSS_noopenmp.mexmaci
D       old/cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
D       old/cg_glm_get_Beta_ResSS_noopenmp.mexw32
D       old/cg_glm_get_Beta_ResSS_noopenmp.mexw64
D       old/spm_datatypes.h
D       old/spm_getdata.c
D       old/spm_getdata.h
D       old/spm_getdata.mexw32.obj
D       old/spm_getdata.mexw64.obj
D       old/spm_make_lookup.c
D       old/spm_make_lookup.h
D       old/spm_make_lookup.mexw32.obj
D       old/spm_make_lookup.mexw64.obj
D       old/spm_mapping.c
D       old/spm_mapping.h
D       old/spm_mapping.mexw32.obj
D       old/spm_mapping.mexw64.obj
D       old/spm_vol_access.c
D       old/spm_vol_access.h
D       old/spm_vol_access.mexw32.obj
D       old/spm_vol_access.mexw64.obj
D       old/spm_vol_utils.c
D       old/utils_double.mexw32.obj
D       old/utils_double.mexw64.obj
D       old/utils_double_s.mexw32.obj
D       old/utils_double_s.mexw64.obj
D       old/utils_float.mexw32.obj
D       old/utils_float.mexw64.obj
D       old/utils_float_s.mexw32.obj
D       old/utils_float_s.mexw64.obj
D       old/utils_int.mexw32.obj
D       old/utils_int.mexw64.obj
D       old/utils_int_s.mexw32.obj
D       old/utils_int_s.mexw64.obj
D       old/utils_schar.mexw32.obj
D       old/utils_schar.mexw64.obj
D       old/utils_short.mexw32.obj
D       old/utils_short.mexw64.obj
D       old/utils_short_s.mexw32.obj
D       old/utils_short_s.mexw64.obj
D       old/utils_uchar.mexw32.obj
D       old/utils_uchar.mexw64.obj
D       old/utils_uint.mexw32.obj
D       old/utils_uint.mexw64.obj
D       old/utils_uint_s.mexw32.obj
D       old/utils_uint_s.mexw64.obj
D       old/utils_ushort.mexw32.obj
D       old/utils_ushort.mexw64.obj
D       old/utils_ushort_s.mexw32.obj
D       old/utils_ushort_s.mexw64.obj
D       questions.txt
        > moved to trunk/questions.txt
D       snpm_P_FDR.m
        > moved to trunk/snpm_P_FDR.m
D       spm_TFCE.m
        > moved to trunk/spm_TFCE.m
D       svn_ci_log
        > moved to trunk/svn_ci_log
A       tag
D       tbx_cfg_tfce_estimate.m
        > moved to trunk/tbx_cfg_tfce_estimate.m
D       tfceMex.c
        > moved to trunk/tfceMex.c
D       tfceMex.m
        > moved to trunk/tfceMex.m
D       tfceMex.mexa64
        > moved to trunk/tfceMex.mexa64
D       tfceMex.mexglx
        > moved to trunk/tfceMex.mexglx
D       tfceMex.mexmaci
        > moved to trunk/tfceMex.mexmaci
D       tfceMex.mexmaci64
        > moved to trunk/tfceMex.mexmaci64
D       tfceMex.mexw32
        > moved to trunk/tfceMex.mexw32
D       tfceMex.mexw64
        > moved to trunk/tfceMex.mexw64
D       tfceMex_noopenmp.mexa64
        > moved to trunk/tfceMex_noopenmp.mexa64
D       tfceMex_noopenmp.mexglx
        > moved to trunk/tfceMex_noopenmp.mexglx
D       tfceMex_noopenmp.mexmaci
        > moved to trunk/tfceMex_noopenmp.mexmaci
D       tfceMex_noopenmp.mexmaci64
        > moved to trunk/tfceMex_noopenmp.mexmaci64
D       tfceMex_noopenmp.mexw32
        > moved to trunk/tfceMex_noopenmp.mexw32
D       tfceMex_noopenmp.mexw64
        > moved to trunk/tfceMex_noopenmp.mexw64
D       tfceMex_pthread.c
        > moved to trunk/tfceMex_pthread.c
D       tfceMex_pthread.m
        > moved to trunk/tfceMex_pthread.m
D       tfceMex_pthread.mexa64
        > moved to trunk/tfceMex_pthread.mexa64
D       tfceMex_pthread.mexmaci64
        > moved to trunk/tfceMex_pthread.mexmaci64
D       tfceMex_pthread.mexw64
        > moved to trunk/tfceMex_pthread.mexw64
D       tfce_mesh.m
        > moved to trunk/tfce_mesh.m
D       todo
        > moved to trunk/todo
A       trunk
A  +    trunk/CHANGES.txt
        > moved from CHANGES.txt
A  +    trunk/Contents_info.txt
        > moved from Contents_info.txt
A  +    trunk/INSTALL_info.txt
        > moved from INSTALL_info.txt
A  +    trunk/Makefile
        > moved from Makefile
A  +    trunk/SPM-Designs-Permutation.doc
        > moved from SPM-Designs-Permutation.doc
A  +    trunk/TFCE.txt
        > moved from TFCE.txt
A  +    trunk/cg_get_tfce_results.m
        > moved from cg_get_tfce_results.m
A  +    trunk/cg_progress.m
        > moved from cg_progress.m
A  +    trunk/cg_tfce_estimate.m
        > moved from cg_tfce_estimate.m
A  +    trunk/cg_tfce_list.m
        > moved from cg_tfce_list.m
A  +    trunk/cg_tfce_results.m
        > moved from cg_tfce_results.m
A  +    trunk/cg_tfce_update.m
        > moved from cg_tfce_update.m
A  +    trunk/compile.m
        > moved from compile.m
A  +    trunk/old
        > moved from old
A  +    trunk/questions.txt
        > moved from questions.txt
A  +    trunk/snpm_P_FDR.m
        > moved from snpm_P_FDR.m
A  +    trunk/spm_TFCE.m
        > moved from spm_TFCE.m
A  +    trunk/svn_ci_log
        > moved from svn_ci_log
A  +    trunk/tbx_cfg_tfce_estimate.m
        > moved from tbx_cfg_tfce_estimate.m
A  +    trunk/tfceMex.c
        > moved from tfceMex.c
A  +    trunk/tfceMex.m
        > moved from tfceMex.m
A  +    trunk/tfceMex.mexa64
        > moved from tfceMex.mexa64
A  +    trunk/tfceMex.mexglx
        > moved from tfceMex.mexglx
A  +    trunk/tfceMex.mexmaci
        > moved from tfceMex.mexmaci
A  +    trunk/tfceMex.mexmaci64
        > moved from tfceMex.mexmaci64
A  +    trunk/tfceMex.mexw32
        > moved from tfceMex.mexw32
A  +    trunk/tfceMex.mexw64
        > moved from tfceMex.mexw64
A  +    trunk/tfceMex_noopenmp.mexa64
        > moved from tfceMex_noopenmp.mexa64
A  +    trunk/tfceMex_noopenmp.mexglx
        > moved from tfceMex_noopenmp.mexglx
A  +    trunk/tfceMex_noopenmp.mexmaci
        > moved from tfceMex_noopenmp.mexmaci
A  +    trunk/tfceMex_noopenmp.mexmaci64
        > moved from tfceMex_noopenmp.mexmaci64
A  +    trunk/tfceMex_noopenmp.mexw32
        > moved from tfceMex_noopenmp.mexw32
A  +    trunk/tfceMex_noopenmp.mexw64
        > moved from tfceMex_noopenmp.mexw64
A  +    trunk/tfceMex_pthread.c
        > moved from tfceMex_pthread.c
A  +    trunk/tfceMex_pthread.m
        > moved from tfceMex_pthread.m
A  +    trunk/tfceMex_pthread.mexa64
        > moved from tfceMex_pthread.mexa64
A  +    trunk/tfceMex_pthread.mexmaci64
        > moved from tfceMex_pthread.mexmaci64
A  +    trunk/tfceMex_pthread.mexw64
        > moved from tfceMex_pthread.mexw64
A  +    trunk/tfce_mesh.m
        > moved from tfce_mesh.m
A  +    trunk/todo
        > moved from todo



------------------------------------------------------------------------
r95 | gaser | 2016-09-12 10:16:51 +0200 (Mon, 12 Sep 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_get_tfce_results.m
M       cg_tfce_results.m

Changed: Changed call to TFCE toolbox and updated results section
according to newer spm_results_ui.m.


------------------------------------------------------------------------
r94 | gaser | 2016-09-12 02:58:14 +0200 (Mon, 12 Sep 2016) | 9 lines

Changed paths:
M       CHANGES.txt
A       INSTALL_info.txt
R  +    Makefile
D       Makefile.tfce
D       Makefile.var

Changed: Makefile and installation routine updated.

------------------------------------------------------------------------
r93 | gaser | 2016-08-24 14:38:31 +0200 (Wed, 24 Aug 2016) | 96 lines

Changed paths:
M       CHANGES.txt
M       cg_get_tfce_results.m
D       cg_glm_get_Beta_ResSS.c
D       cg_glm_get_Beta_ResSS.m
D       cg_glm_get_Beta_ResSS.mexa64
D       cg_glm_get_Beta_ResSS.mexglx
D       cg_glm_get_Beta_ResSS.mexmaci
D       cg_glm_get_Beta_ResSS.mexmaci64
D       cg_glm_get_Beta_ResSS.mexw32
D       cg_glm_get_Beta_ResSS.mexw64
D       cg_glm_get_Beta_ResSS_noopenmp.mexa64
D       cg_glm_get_Beta_ResSS_noopenmp.mexglx
D       cg_glm_get_Beta_ResSS_noopenmp.mexmaci
D       cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
D       cg_glm_get_Beta_ResSS_noopenmp.mexw32
D       cg_glm_get_Beta_ResSS_noopenmp.mexw64
M       cg_tfce_list.m
M       cg_tfce_results.m
A       old
A  +    old/cg_glm_get_Beta_ResSS.c
A  +    old/cg_glm_get_Beta_ResSS.m
A  +    old/cg_glm_get_Beta_ResSS.mexa64
A  +    old/cg_glm_get_Beta_ResSS.mexglx
A  +    old/cg_glm_get_Beta_ResSS.mexmaci
A  +    old/cg_glm_get_Beta_ResSS.mexmaci64
A  +    old/cg_glm_get_Beta_ResSS.mexw32
A  +    old/cg_glm_get_Beta_ResSS.mexw64
A  +    old/cg_glm_get_Beta_ResSS_noopenmp.mexa64
A  +    old/cg_glm_get_Beta_ResSS_noopenmp.mexglx
A  +    old/cg_glm_get_Beta_ResSS_noopenmp.mexmaci
A  +    old/cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
A  +    old/cg_glm_get_Beta_ResSS_noopenmp.mexw32
A  +    old/cg_glm_get_Beta_ResSS_noopenmp.mexw64
A  +    old/spm_datatypes.h
A  +    old/spm_getdata.c
A  +    old/spm_getdata.h
A       old/spm_getdata.mexw32.obj
A       old/spm_getdata.mexw64.obj
A  +    old/spm_make_lookup.c
A  +    old/spm_make_lookup.h
A       old/spm_make_lookup.mexw32.obj
A       old/spm_make_lookup.mexw64.obj
A  +    old/spm_mapping.c
A  +    old/spm_mapping.h
A       old/spm_mapping.mexw32.obj
A       old/spm_mapping.mexw64.obj
A  +    old/spm_vol_access.c
A  +    old/spm_vol_access.h
A       old/spm_vol_access.mexw32.obj
A       old/spm_vol_access.mexw64.obj
A  +    old/spm_vol_utils.c
A       old/utils_double.mexw32.obj
A       old/utils_double.mexw64.obj
A       old/utils_double_s.mexw32.obj
A       old/utils_double_s.mexw64.obj
A       old/utils_float.mexw32.obj
A       old/utils_float.mexw64.obj
A       old/utils_float_s.mexw32.obj
A       old/utils_float_s.mexw64.obj
A       old/utils_int.mexw32.obj
A       old/utils_int.mexw64.obj
A       old/utils_int_s.mexw32.obj
A       old/utils_int_s.mexw64.obj
A       old/utils_schar.mexw32.obj
A       old/utils_schar.mexw64.obj
A       old/utils_short.mexw32.obj
A       old/utils_short.mexw64.obj
A       old/utils_short_s.mexw32.obj
A       old/utils_short_s.mexw64.obj
A       old/utils_uchar.mexw32.obj
A       old/utils_uchar.mexw64.obj
A       old/utils_uint.mexw32.obj
A       old/utils_uint.mexw64.obj
A       old/utils_uint_s.mexw32.obj
A       old/utils_uint_s.mexw64.obj
A       old/utils_ushort.mexw32.obj
A       old/utils_ushort.mexw64.obj
A       old/utils_ushort_s.mexw32.obj
A       old/utils_ushort_s.mexw64.obj
R  +    spm_TFCE.m
D       spm_datatypes.h
D       spm_getdata.c
D       spm_getdata.h
D       spm_make_lookup.c
D       spm_make_lookup.h
D       spm_mapping.c
D       spm_mapping.h
D       spm_vol_access.c
D       spm_vol_access.h
D       spm_vol_utils.c

(1) Changed: Moved un-used functions to old folder.
(2) Fixed: Corrected text output of result table.
(3) Changed: Added support for inverse contrasts.

------------------------------------------------------------------------
r92 | gaser | 2016-08-23 17:16:57 +0200 (Tue, 23 Aug 2016) | 18 lines

Changed paths:
M       CHANGES.txt
M       cg_get_tfce_results.m
M       cg_tfce_estimate.m
M       cg_tfce_results.m
MM      tfceMex_pthread.c
MM      tfceMex_pthread.m
 M      tfceMex_pthread.mexa64
 M      tfceMex_pthread.mexmaci64
 M      tfceMex_pthread.mexw64
M       tfce_mesh.m

(1) Changed: Added support for F-test.
(2) Changed: Added inverse contrast to distribution plot.
(3) Fixed: Atlas menu is only displayed for volume data.
(4) Changed: TFCE calculation is now faster if no neg. values are present.
(5) Changed: Removed variance smoothing.

------------------------------------------------------------------------
r91 | gaser | 2016-08-12 15:16:17 +0200 (Fri, 12 Aug 2016) | 6 lines

Changed paths:
M       CHANGES.txt
M       tfceMex_pthread.c

Changed: Data type of dims is now int.

------------------------------------------------------------------------
r90 | gaser | 2016-08-01 20:05:57 +0200 (Mon, 01 Aug 2016) | 25 lines

Changed paths:
M       CHANGES.txt
M       Makefile.tfce
M       cg_progress.m
M       cg_tfce_estimate.m
M       compile.m
M       tbx_cfg_tfce_estimate.m
M       tfceMex.m
A       tfceMex_pthread.c
A       tfceMex_pthread.m
A       tfceMex_pthread.mexa64
A       tfceMex_pthread.mexmaci64
A       tfceMex_pthread.mexw64
M       tfce_mesh.m

(1) Changed: The step size dh is now estimatet more balanced by using 
    individual dh's for each t-map.
(2) Changed: Main function cg_tfce_estimate is now loading all data once into a 
    matrix Y. This is resulting in a large speed improvement but memory 
    demand increases with sample size.
(3) Changed: Now use pthread for tfce calculation with new tfceMex_pthread.c.
(4) Fixed: Issues with new matlab version and cg_progress.m
(5) Changed: Graphical output is now only drawn 100 times to save time.


------------------------------------------------------------------------
r89 | gaser | 2016-06-22 17:21:42 +0200 (Wed, 22 Jun 2016) | 9 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_list.m
M       cg_tfce_results.m
 M      todo

Changed: Added atlas function to results.


------------------------------------------------------------------------
r88 | gaser | 2016-04-11 11:53:27 +0200 (Mon, 11 Apr 2016) | 7 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_results.m

Changed: Added gifit functionality for saving thresholded results.


------------------------------------------------------------------------
r87 | gaser | 2016-01-19 00:49:27 +0100 (Tue, 19 Jan 2016) | 7 lines

Changed paths:
M       CHANGES.txt
A       todo

New: todo file


------------------------------------------------------------------------
r86 | gaser | 2015-12-08 11:35:21 +0100 (Tue, 08 Dec 2015) | 12 lines

Changed paths:
M       CHANGES.txt
M       cg_glm_get_Beta_ResSS.c
M       cg_glm_get_Beta_ResSS.mexmaci64
M       cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
M       compile.m
M       tfceMex.mexmaci64
M       tfceMex_noopenmp.mexmaci64

(1) Changed: comnpile.m to consider new OSX
(2) Changed: recompiled mexmaci64 code

------------------------------------------------------------------------
r85 | gaser | 2015-12-01 11:55:55 +0100 (Tue, 01 Dec 2015) | 15 lines

Changed paths:
M       CHANGES.txt
M       SPM-Designs-Permutation.doc
 M      cg_glm_get_Beta_ResSS_noopenmp.mexa64
 M      cg_glm_get_Beta_ResSS_noopenmp.mexglx
 M      cg_glm_get_Beta_ResSS_noopenmp.mexmaci
 M      cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
 M      cg_glm_get_Beta_ResSS_noopenmp.mexw32
 M      cg_glm_get_Beta_ResSS_noopenmp.mexw64
M       cg_tfce_estimate.m
M       cg_tfce_list.m

Fixed: Solved issue with newer matlab version regarding the check for Fgraph 
in cg_tfce_list.m. Thanks to Joshua Balsters for pointing to this issue.

------------------------------------------------------------------------
r84 | gaser | 2015-11-25 11:31:34 +0100 (Wed, 25 Nov 2015) | 10 lines

Changed paths:
M       CHANGES.txt
M       Makefile.tfce
M       cg_tfce_estimate.m

(1) Added correction of xX for some weird designs where iH and iB are
    not correct.
(2) Added test_mode parameter to run permutations without data.
(3) Corrected some inconsistencies for longitudinal designs.

------------------------------------------------------------------------
r83 | gaser | 2015-11-24 13:26:22 +0100 (Tue, 24 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
A       cg_glm_get_Beta_ResSS_noopenmp.mexa64
A       cg_glm_get_Beta_ResSS_noopenmp.mexglx
A       cg_glm_get_Beta_ResSS_noopenmp.mexmaci
A       cg_glm_get_Beta_ResSS_noopenmp.mexmaci64
A       cg_glm_get_Beta_ResSS_noopenmp.mexw32
A       cg_glm_get_Beta_ResSS_noopenmp.mexw64

Added cg_glm_get_Beta_ResSS_noopenmp.mex* files.

------------------------------------------------------------------------
r82 | gaser | 2015-11-04 14:07:20 +0100 (Wed, 04 Nov 2015) | 11 lines

Changed paths:
M       CHANGES.txt
M       SPM-Designs-Permutation.doc
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

(1) tbx_cfg_tfce_estimate.m had some entries that were only working for SPM12.
    This is now solved. Thanks to Lindsay Hanford for pointing to that error.
(2) Updated help text.
(3) Added check whether size of mask image and data fit.

------------------------------------------------------------------------
r81 | gaser | 2015-11-02 22:29:43 +0100 (Mon, 02 Nov 2015) | 8 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m

(1) In cg_tfce_estimate.m ind_data_defined was not correctly estimated for
    some designs.
(2) Updated table.

------------------------------------------------------------------------
r80 | gaser | 2015-11-02 22:22:14 +0100 (Mon, 02 Nov 2015) | 10 lines

Changed paths:
M       CHANGES.txt
M       SPM-Designs-Permutation.doc
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m

(1) In cg_tfce_estimate.m ind_data_defined was not correctly estimated for
    some designs.
(2) Updated table.

------------------------------------------------------------------------
r79 | gaser | 2015-10-29 09:19:18 +0100 (Thu, 29 Oct 2015) | 10 lines

Changed paths:
M       CHANGES.txt
M       cg_tfce_estimate.m
M       svn_ci_log

(1) If either no positive or negative T or TFCE-values are found FDR
    correction crashed This is now solved (thanks to Nikolaos Koustlsouleris
    for pointing to that issue).
(2) Use try-commands to allow batch mode without graphical output.

------------------------------------------------------------------------
r78 | gaser | 2015-09-10 12:23:01 +0200 (Thu, 10 Sep 2015) | 24 lines

Changed paths:
 M      SPM-Designs-Permutation.doc
M       cg_glm_get_Beta_ResSS.mexw32
M       cg_glm_get_Beta_ResSS.mexw64
M       cg_tfce_estimate.m
M       tbx_cfg_tfce_estimate.m
M       tfceMex.c
M       tfceMex.m
M       tfceMex.mexa64
M       tfceMex.mexglx
M       tfceMex.mexmaci64
M       tfceMex.mexw32
M       tfceMex.mexw64
M       tfceMex_noopenmp.mexa64
M       tfceMex_noopenmp.mexglx
M       tfceMex_noopenmp.mexmaci64
M       tfceMex_noopenmp.mexw32
M       tfceMex_noopenmp.mexw64
M       tfce_mesh.m

(1) Added option for TBSS data with 2D optimization.
(2) Changed E-parameter for meshes to 1 in tfce_mesh.m.


------------------------------------------------------------------------
r77 | gaser | 2015-06-26 15:32:07 +0200 (Fri, 26 Jun 2015) | 7 lines

Changed paths:
M       cg_tfce_estimate.m

Fixed bug in cg_tfce_estimate.m for multiple regressions (Thanks to Marcel
Zwiers).


------------------------------------------------------------------------
r76 | gaser | 2015-06-17 11:00:05 +0200 (Wed, 17 Jun 2015) | 8 lines

Changed paths:
A       SPM-Designs-Permutation.doc
M       cg_tfce_estimate.m

(1) Again corrected bug with exch_blocks in cg_tfce_estimate.m.
(2) Added SPM-Designs-Permutation.doc.


------------------------------------------------------------------------
r75 | gaser | 2015-06-15 11:03:42 +0200 (Mon, 15 Jun 2015) | 8 lines

Changed paths:
M       cg_tfce_estimate.m

Corrected bug with exch_blocks in cg_tfce_estimate.m for repeated measurements.




------------------------------------------------------------------------
r74 | gaser | 2015-02-09 09:05:42 +0100 (Mon, 09 Feb 2015) | 9 lines

Changed paths:
M       cg_tfce_estimate.m
M       tfceMex.c

Corrected bug with exch_blocks in cg_tfce_estimate.m.




------------------------------------------------------------------------
r73 | gaser | 2014-12-01 13:27:00 +0100 (Mon, 01 Dec 2014) | 9 lines

Changed paths:
M       cg_tfce_estimate.m

(1) Always display permuted design matrix now instead of t-stuff.
(3) Corrected # of permutations for sparse long. design where not all
    time points are defined.



------------------------------------------------------------------------
r72 | gaser | 2014-11-28 17:28:54 +0100 (Fri, 28 Nov 2014) | 9 lines

Changed paths:
M       cg_tfce_estimate.m

(1) Added opportunity to estimate exchaneability block labels for repeated
    Anova designs.
(2) Corrected estimation of # of permutations for repeated anova.



------------------------------------------------------------------------
r71 | gaser | 2014-11-14 10:41:31 +0100 (Fri, 14 Nov 2014) | 10 lines

Changed paths:
M       cg_progress.m
M       cg_tfce_estimate.m
MM      tfce_mesh.m

(1) Some cosmetic changes to cg_tfce_estimate.m.
(2) cg_tfce_estimate can now also deal with correlational designs with single
    regressor and dummy block before covariate.


------------------------------------------------------------------------
r70 | gaser | 2014-11-13 11:44:52 +0100 (Thu, 13 Nov 2014) | 8 lines

Changed paths:
M       cg_get_tfce_results.m
M       cg_tfce_estimate.m

Corrected issues with different file extensions. Now the extension of the 
previous analysis will be used.


------------------------------------------------------------------------
r69 | gaser | 2014-11-12 15:08:52 +0100 (Wed, 12 Nov 2014) | 30 lines

Changed paths:
M       Makefile.tfce
M       cg_get_tfce_results.m
M       cg_glm_get_Beta_ResSS.mexmaci64
!       cg_glm_get_Beta_ResSS.mexw32
!       cg_glm_get_Beta_ResSS.mexw64
M       cg_tfce_estimate.m
M       cg_tfce_list.m
M       cg_tfce_results.m
M       compile.m
M       spm_TFCE.m
M       tbx_cfg_tfce_estimate.m
M       tfceMex.c
M       tfceMex.mexa64
M       tfceMex.mexglx
M       tfceMex.mexmaci64
M       tfceMex.mexw32
M       tfceMex.mexw64
M       tfceMex_noopenmp.mexa64
M       tfceMex_noopenmp.mexglx
M       tfceMex_noopenmp.mexmaci64
M       tfceMex_noopenmp.mexw32
M       tfceMex_noopenmp.mexw64
A       tfce_mesh.m

(1) Added support for surfaces!
(2) Made several changes according to new spm12 code.
(3) TFCE is now running for SPM8 and SPM12.


------------------------------------------------------------------------
r68 | gaser | 2014-07-28 14:34:27 +0200 (Mon, 28 Jul 2014) | 6 lines

Changed paths:
M       cg_tfce_estimate.m
M       compile.m

Handle all multiple regression designs.

------------------------------------------------------------------------
r67 | gaser | 2014-04-15 14:27:56 +0200 (Tue, 15 Apr 2014) | 25 lines

Changed paths:
M       cg_glm_get_Beta_ResSS.c
M       cg_glm_get_Beta_ResSS.mexa64
M       cg_glm_get_Beta_ResSS.mexglx
M       cg_glm_get_Beta_ResSS.mexmaci64
M       cg_glm_get_Beta_ResSS.mexw32
M       cg_glm_get_Beta_ResSS.mexw64
M       cg_tfce_estimate.m
M       compile.m
M       tfceMex.c
M       tfceMex.mexa64
M       tfceMex.mexglx
M       tfceMex.mexmaci64
M       tfceMex.mexw32
M       tfceMex.mexw64
M       tfceMex_noopenmp.mexa64
M       tfceMex_noopenmp.mexglx
M       tfceMex_noopenmp.mexmaci64
M       tfceMex_noopenmp.mexw32
M       tfceMex_noopenmp.mexw64

(1) Stepsize for TFCE is now estimated using unpermuted data and is then used
    for all permuted data. Thanks to Chris Rorden for pointing to that issue.
(2) Recompiled windows versions.

------------------------------------------------------------------------
r66 | gaser | 2014-01-24 16:36:58 +0100 (Fri, 24 Jan 2014) | 9 lines

Changed paths:
M       cg_glm_get_Beta_ResSS.mexmaci
M       cg_tfce_estimate.m
M       tfceMex.mexmaci
M       tfceMex_noopenmp.mexmaci

(1) Added support for multiple regression designs where spm.xX.iH is empty.
(2) Compiled for mexmaci.

------------------------------------------------------------------------
r65 | gaser | 2013-10-11 08:40:21 +0200 (Fri, 11 Oct 2013) | 7 lines

Changed paths:
M       cg_tfce_estimate.m

(1) Constrain contrasts (and exchangeability blocks) to effects of interest 
    only.
(2) Debug mode now shows color-coded exchangeability blocks).

------------------------------------------------------------------------
r64 | gaser | 2013-10-01 17:09:01 +0200 (Tue, 01 Oct 2013) | 6 lines

Changed paths:
M       spm_TFCE.m
M       cg_get_tfce_results.m

Removed some minor bugs.

------------------------------------------------------------------------
r63 | gaser | 2013-10-01 16:45:40 +0200 (Tue, 01 Oct 2013) | 6 lines

Changed paths:
M       Makefile.tfce
M       CHANGES.txt

Added update to install function in Makefile.tfce.

------------------------------------------------------------------------
r62 | gaser | 2013-10-01 16:29:17 +0200 (Tue, 01 Oct 2013) | 16 lines

Changed paths:
M       cg_tfce_estimate.m
D       TFCE.fig
M       Contents_info.txt
!M      spm_TFCE.m
M       Makefile.tfce
M       tbx_cfg_tfce_estimate.m
D       TFCE.m
D       cg_getTFCE.m
M       CHANGES.txt
A  +    cg_get_tfce_results.m
M       cg_tfce_results.m

(1) Added option for additional mask image to provide SVC.
(2) Changed GUI back to file menu.

------------------------------------------------------------------------
r61 | gaser | 2013-05-14 10:46:09 +0200 (Tue, 14 May 2013) | 17 lines

Changed paths:
A  +    cg_tfce_estimate.m
D       tfce.fig
A  +    TFCE.fig
M       Contents_info.txt
D       spm_tfce.m
A  +    spm_TFCE.m
M       Makefile.tfce
M       TFCE.txt
M       tbx_cfg_tfce_estimate.m
D       tfce.m
A  +    TFCE.m
D       cg_run_tfce_estimate.m

(1) Renamed tfce to TFCE.
(2) Renamed cg_run_tfce_estimate to cg_tfce_estimate.m.

------------------------------------------------------------------------
r60 | gaser | 2013-03-12 18:11:04 +0100 (Tue, 12 Mar 2013) | 8 lines

Changed paths:
M       tbx_cfg_tfce_estimate.m
M       cg_progress.m
M       cg_run_tfce_estimate.m

(1) Added some notes.
(2) Figure now also prints analysis path and processing time.

------------------------------------------------------------------------
r59 | gaser | 2013-01-29 16:45:20 +0100 (Tue, 29 Jan 2013) | 6 lines

Changed paths:
M       cg_run_tfce_estimate.m

Corrected calculation of # of permutations for large n's and designs with
just one subject in cg_run_tfce_estimate.m

------------------------------------------------------------------------
r58 | gaser | 2013-01-29 10:55:47 +0100 (Tue, 29 Jan 2013) | 5 lines

Changed paths:
M       cg_run_tfce_estimate.m

Removed two typos in cg_run_tfce_estimate.m

------------------------------------------------------------------------
r57 | gaser | 2012-07-25 10:51:09 +0200 (Wed, 25 Jul 2012) | 6 lines

Changed paths:
M       tfceMex.c
M       cg_run_tfce_estimate.m

Removed 2nd warning for not yet supported whitening.

------------------------------------------------------------------------
r56 | gaser | 2012-02-10 14:48:57 +0100 (Fri, 10 Feb 2012) | 32 lines

Changed paths:
M       cg_glm_get_Beta_ResSS.c
M       tfceMex.mexw64
M       cg_glm_get_Beta_ResSS.mexw32
M       tfce.fig
M       cg_glm_get_Beta_ResSS.mexmaci64
M       Makefile.tfce
M       tfceMex_noopenmp.mexw64
M       tfceMex_noopenmp.mexmaci64
M       tbx_cfg_tfce_estimate.m
M       cg_glm_get_Beta_ResSS.mexglx
M       cg_glm_get_Beta_ResSS.mexa64
M       tfceMex.c
M       tfceMex.mexw32
M       compile.m
M       cg_glm_get_Beta_ResSS.mexmaci
M       cg_getTFCE.m
M       tfceMex.mexmaci64
M       tfceMex_noopenmp.mexmaci
M       cg_glm_get_Beta_ResSS.mexw64
M       tfceMex_noopenmp.mexw32
M       tfceMex.mexa64
M       tfceMex.mexglx
M       cg_run_tfce_estimate.m
M       tfceMex_noopenmp.mexa64
M       tfceMex_noopenmp.mexglx
M       tfceMex.mexmaci

(1) Multi-threading using OpenMP!
(2) Added some options for batch mode.
(3) Many small changes in cg_run_tfce_estimate.m

------------------------------------------------------------------------
r55 | gaser | 2012-02-10 01:08:57 +0100 (Fri, 10 Feb 2012) | 5 lines

Changed paths:
M       cg_run_tfce_estimate.m

Solved issues with Anovas with > 2 groups and contrasts for > 2 columns.

------------------------------------------------------------------------
r54 | gaser | 2011-11-18 21:48:44 +0100 (Fri, 18 Nov 2011) | 6 lines

Changed paths:
MM      tfce.fig
 M      tfce.m

Corrected size of figure.

------------------------------------------------------------------------
r53 | gaser | 2011-11-18 21:02:04 +0100 (Fri, 18 Nov 2011) | 7 lines

Changed paths:
M       Makefile.tfce
M       cg_getTFCE.m
M       CHANGES.txt

Removed cg_tfce_estimate from Makefile.

------------------------------------------------------------------------
r52 | gaser | 2011-07-27 10:38:45 +0200 (Wed, 27 Jul 2011) | 7 lines

Changed paths:
A      tfce.fig
M      Makefile.tfce
A      tfce.m

Changed GUI style from menubar to additional window.

------------------------------------------------------------------------
r51 | gaser | 2011-07-25 12:45:19 +0200 (Mon, 25 Jul 2011) | 6 lines

Changed paths:
M      cg_getTFCE.m

Removed bug in cg_getTFCE.m that caused, that also values below threshold were
reported.

------------------------------------------------------------------------
r50 | gaser | 2011-06-21 17:01:54 +0200 (Tue, 21 Jun 2011) | 54 lines

Changed paths:
MM     cg_tfce_list.m
MM     spm_vol_utils.c
MM     spm_vol_access.c
 M     cg_glm_get_Beta_ResSS.c
 M     tfceMex.mexw64
 M     cg_glm_get_Beta_ResSS.mexw32
MM     Contents_info.txt
MM     spm_vol_access.h
MM     cg_tfce_update.m
 M     spm_tfce.m
 M     cg_glm_get_Beta_ResSS.m
 M     cg_glm_get_Beta_ResSS.mexmaci64
MM     Makefile.tfce
 M     TFCE.txt
 M     tfceMex_noopenmp.mexw64
 M     tfceMex_noopenmp.mexmaci64
MM     tbx_cfg_tfce_estimate.m
 M     cg_glm_get_Beta_ResSS.mexglx
 M     cg_glm_get_Beta_ResSS.mexa64
 M     cg_progress.m
 M     questions.txt
MM     spm_getdata.c
MM     tfceMex.c
MM     Makefile
MM     spm_getdata.h
 M     tfceMex.mexw32
MM     svn_ci_log
MM     snpm_P_FDR.m
 M     compile.m
 M     cg_glm_get_Beta_ResSS.mexmaci
MM     cg_getTFCE.m
MM     tfceMex.m
 M     CHANGES.txt
 M     tfceMex.mexmaci64
 M     tfceMex_noopenmp.mexmaci
 M     cg_glm_get_Beta_ResSS.mexw64
 M     tfceMex_noopenmp.mexw32
MM     spm_mapping.c
 M     tfceMex.mexa64
 M     tfceMex.mexglx
MM     spm_mapping.h
MM     spm_datatypes.h
MM     Makefile.var
MM     cg_run_tfce_estimate.m
MM     spm_make_lookup.c
 M     cg_tfce_results.m
 M     tfceMex_noopenmp.mexa64
 M     tfceMex_noopenmp.mexglx
MM     spm_make_lookup.h
 M     tfceMex.mexmaci

Updated svn_ci_log to set svn properties.

------------------------------------------------------------------------
r49 | gaser | 2011-03-31 11:33:45 +0200 (Thu, 31 Mar 2011) | 5 lines

Changed paths:
M      cg_run_tfce_estimate.m

Removed debug code from cg_run_tfce_estimate.m.

------------------------------------------------------------------------
r48 | gaser | 2011-03-31 08:39:43 +0200 (Thu, 31 Mar 2011) | 6 lines

Changed paths:
M      cg_tfce_list.m
M      cg_getTFCE.m

Corrected name of ascii-file, where number of permutations is saved.

------------------------------------------------------------------------
r47 | gaser | 2011-03-30 12:16:31 +0200 (Wed, 30 Mar 2011) | 5 lines

Changed paths:
M      cg_run_tfce_estimate.m

Corrected path of mask-image in cg_run_tfce_estimate.m if folder was changed.

------------------------------------------------------------------------
r46 | gaser | 2011-03-30 10:38:32 +0200 (Wed, 30 Mar 2011) | 10 lines

Changed paths:
D      cg_tfce_estimate.m
D      cg_tfce_estimate_multi.m
M      spm_tfce.m
M      Makefile.tfce
A      tbx_cfg_tfce_estimate.m
A      cg_run_tfce_estimate.m

Added batch mode for TFCE estimate.

------------------------------------------------------------------------
r45 | gaser | 2011-03-03 16:23:05 +0100 (Thu, 03 Mar 2011) | 7 lines

Changed paths:
M      cg_tfce_estimate.m

(1) Check that number of new filenames are correct before saving updated
    SPM.mat in cg_tfce_estimate.m.
(2) Graphical output of histograms slightly changed.

------------------------------------------------------------------------
r44 | gaser | 2011-03-01 22:54:28 +0100 (Tue, 01 Mar 2011) | 5 lines

Changed paths:
M       cg_tfce_estimate.m

Corrected estimation for interaction designs.

------------------------------------------------------------------------
r43 | gaser | 2011-03-01 17:27:46 +0100 (Tue, 01 Mar 2011) | 5 lines

Changed paths:
M      cg_tfce_estimate.m

Removed some debug code.

------------------------------------------------------------------------
r42 | gaser | 2011-03-01 16:48:46 +0100 (Tue, 01 Mar 2011) | 25 lines

Changed paths:
M      cg_tfce_estimate.m
M      tfceMex.mexw64
M      cg_glm_get_Beta_ResSS.mexw32
M      tfceMex_noopenmp.mexw64
M      tfceMex_noopenmp.mexmaci64
M      cg_glm_get_Beta_ResSS.mexa64
M      cg_glm_get_Beta_ResSS.mexglx
M      tfceMex.c
M      tfceMex.mexw32
M      tfceMex.mexmaci64
M      tfceMex_noopenmp.mexmaci
M      cg_glm_get_Beta_ResSS.mexw64
M      tfceMex_noopenmp.mexw32
M      tfceMex.mexa64
M      tfceMex.mexglx
M      tfceMex_noopenmp.mexa64
M      tfceMex_noopenmp.mexglx
M      tfceMex.mexmaci

(1) Allow calculation of tfce-values for inverse contrast (= neg. t-values)
    in tfceMex.c.
(2) Recompiled tfceMex.c.
(3) Allow to use half of permutations for equally sized samples.

------------------------------------------------------------------------
r41 | gaser | 2011-03-01 11:56:07 +0100 (Tue, 01 Mar 2011) | 6 lines

Changed paths:
M      cg_tfce_estimate.m
M      questions.txt

Removed debug entries.

------------------------------------------------------------------------
r40 | gaser | 2011-02-28 17:04:22 +0100 (Mon, 28 Feb 2011) | 11 lines

Changed paths:
M      cg_tfce_list.m
M      cg_tfce_estimate.m
M      Makefile.tfce
M      cg_getTFCE.m
A      CHANGES.txt
M      cg_tfce_results.m

Rather use old estimation of uncorrected p-values, because SnPM and
randomize cause uncorrect p-values.

------------------------------------------------------------------------
r39 | gaser | 2011-02-28 01:03:44 +0100 (Mon, 28 Feb 2011) | 7 lines

Changed paths:
M       cg_tfce_list.m
M       cg_tfce_estimate.m
M       cg_getTFCE.m

Corrected list of p-values.

------------------------------------------------------------------------
r38 | gaser | 2011-02-25 17:12:37 +0100 (Fri, 25 Feb 2011) | 14 lines

Changed paths:
M      cg_tfce_list.m
M      cg_tfce_estimate.m
M      tfceMex.mexw64
M      cg_glm_get_Beta_ResSS.mexw32
M      tfceMex_noopenmp.mexw64
M      tfceMex.mexw32
A      snpm_P_FDR.m
M      cg_getTFCE.m
M      cg_glm_get_Beta_ResSS.mexw64
M      tfceMex_noopenmp.mexw32

New claculation of p-values based on snpm8b.

------------------------------------------------------------------------
r37 | gaser | 2010-12-13 15:01:13 +0100 (Mon, 13 Dec 2010) | 5 lines

Changed paths:
M      cg_tfce_estimate.m

Corrected typo in cg_tfce_estimate.m.

------------------------------------------------------------------------
r36 | gaser | 2010-12-13 10:34:42 +0100 (Mon, 13 Dec 2010) | 5 lines

Changed paths:
M      Makefile.tfce

Updated Makefile.tfce to consider new files tfceMex_noopen.mex*

------------------------------------------------------------------------
r35 | gaser | 2010-12-13 10:32:51 +0100 (Mon, 13 Dec 2010) | 5 lines

Changed paths:
M      Makefile.tfce

Updated Makefile.tfce to consider new files tfceMex_noopen.mex*

------------------------------------------------------------------------
r34 | gaser | 2010-12-13 10:20:12 +0100 (Mon, 13 Dec 2010) | 21 lines

Changed paths:
M      cg_tfce_estimate.m
M      tfceMex.mexw64
M      cg_glm_get_Beta_ResSS.mexw32
A      tfceMex_noopenmp.mexw64
A      tfceMex_noopenmp.mexmaci64
M      cg_glm_get_Beta_ResSS.mexglx
M      tfceMex.mexw32
M      compile.m
M      tfceMex.mexmaci64
A      tfceMex_noopenmp.mexmaci
M      cg_glm_get_Beta_ResSS.mexw64
A      tfceMex_noopenmp.mexw32
M      tfceMex.mexa64
M      tfceMex.mexglx
A      tfceMex_noopenmp.mexa64
A      tfceMex_noopenmp.mexglx
M      tfceMex.mexmaci

Additionally provide tfceMex without multi-threading.

------------------------------------------------------------------------
r33 | gaser | 2010-11-09 23:56:52 +0100 (Tue, 09 Nov 2010) | 8 lines

Changed paths:
M      cg_tfce_estimate.m

Use now check that SPM.xX.K is a structure to decide that the model is a first-
level analysis with temporal autocorrelations.



------------------------------------------------------------------------
r32 | gaser | 2010-11-09 23:55:57 +0100 (Tue, 09 Nov 2010) | 8 lines

Changed paths:
M      Makefile.tfce

Use now check that SPM.xX.K is a structure to decide that the model is a first-
level analysis with temporal autocorrelations.



------------------------------------------------------------------------
r31 | gaser | 2010-10-13 17:23:23 +0200 (Wed, 13 Oct 2010) | 8 lines

Changed paths:
M      cg_tfce_estimate.m
M      cg_getTFCE.m
D      CHANGES.txt
M      tfceMex.mexmaci64

Disabled whitening because of weird effects.

------------------------------------------------------------------------
r30 | gaser | 2010-09-24 23:41:23 +0200 (Fri, 24 Sep 2010) | 8 lines

Changed paths:
M       cg_tfce_estimate.m
M       questions.txt
A  +    compile.m
D       make.m

Updated compile.m to additionally provide a single-threaded version of ifceMex.

------------------------------------------------------------------------
r29 | gaser | 2010-09-16 22:07:12 +0200 (Thu, 16 Sep 2010) | 11 lines

Changed paths:
M      tfceMex.mexw64
M      cg_glm_get_Beta_ResSS.mexw32
A      questions.txt
M      tfceMex.c
M      tfceMex.mexw32
M      cg_glm_get_Beta_ResSS.mexw64

Replaced fprintf by printf in tfceMex.c for correct windows output.


------------------------------------------------------------------------
r28 | gaser | 2010-08-25 10:34:05 +0200 (Wed, 25 Aug 2010) | 5 lines

Changed paths:
M      cg_tfce_estimate.m

Some cosmetic changes to cg_tfce_estimate.m.

------------------------------------------------------------------------
r27 | gaser | 2010-08-23 01:35:42 +0200 (Mon, 23 Aug 2010) | 8 lines

Changed paths:
M       tfceMex.c
!       cg_glm_get_Beta_ResSS.mexmaci
M       make.m
!       tfceMex.mexmaci

Updated OPENMP-flags in tfceMex.c

------------------------------------------------------------------------
r26 | gaser | 2010-08-13 12:39:27 +0200 (Fri, 13 Aug 2010) | 5 lines

Changed paths:
M      cg_tfce_estimate.m

Use try-command for calling tfceMex because compilations are not yet ready.

------------------------------------------------------------------------
r25 | gaser | 2010-08-13 12:37:18 +0200 (Fri, 13 Aug 2010) | 8 lines

Changed paths:
M      cg_tfce_estimate.m
M      tfceMex.c
M      tfceMex.m
M      tfceMex.mexmaci64

Added option to print # of processors in tfceMex.c

------------------------------------------------------------------------
r24 | gaser | 2010-08-11 17:24:51 +0200 (Wed, 11 Aug 2010) | 18 lines

Changed paths:
M      tfceMex.mexw64
M      cg_glm_get_Beta_ResSS.mexw32
M      Makefile.tfce
M      cg_glm_get_Beta_ResSS.mexa64
M      cg_glm_get_Beta_ResSS.mexglx
M      tfceMex.c
M      tfceMex.mexw32
M      tfceMex.mexmaci64
M      cg_glm_get_Beta_ResSS.mexw64
M      tfceMex.mexa64
M      tfceMex.mexglx
M      make.m
M      tfceMex.mexmaci

(1) Compiled tfceMex with OpenMP support.
(2) Updated make.m to provide compilations for different systems.

------------------------------------------------------------------------
r23 | gaser | 2010-08-11 11:15:10 +0200 (Wed, 11 Aug 2010) | 8 lines

Changed paths:
M      cg_tfce_estimate.m
M      Makefile.tfce
A      cg_progress.m

(1) Added cg_pogress.m for estimating remaining processing time.
(2) Updated cg_tfce_estimate.m for use of cg_progress.m.

------------------------------------------------------------------------
r22 | gaser | 2010-08-10 14:08:38 +0200 (Tue, 10 Aug 2010) | 9 lines

Changed paths:
M      Contents_info.txt
A      cg_tfce_update.m
M      spm_tfce.m
M      Makefile.tfce

(1) Added update function.
(2) Updated Contents_info.txt

------------------------------------------------------------------------
r21 | gaser | 2010-08-10 10:47:45 +0200 (Tue, 10 Aug 2010) | 8 lines

Changed paths:
M      cg_tfce_list.m
M      cg_tfce_estimate.m
M      cg_getTFCE.m

(1) Remaining time for estimation is printed.
(2) Numbers of permutations are saved in spmTFCE_000x.txt file.

------------------------------------------------------------------------
r20 | gaser | 2010-08-09 09:32:44 +0200 (Mon, 09 Aug 2010) | 11 lines

Changed paths:
M      cg_glm_get_Beta_ResSS.c
M      tfceMex.mexw64
M      Contents_info.txt
M      spm_tfce.m
M      Makefile.tfce
M      cg_glm_get_Beta_ResSS.mexw64

(1) Some cosmetic changes to cg_glm_get_Beta_ResSS.c
(2) Renamed TFCE.man to tfce.man.

------------------------------------------------------------------------
r19 | gaser | 2010-07-30 15:58:59 +0200 (Fri, 30 Jul 2010) | 11 lines

Changed paths:
M      cg_tfce_list.m
M      cg_tfce_estimate.m
A      cg_tfce_estimate_multi.m
M      Makefile.tfce

(1) Added cg_tfce_estimate_multi.m fpr multiple contrasts.
(2) Modified input for cg_tfce_estimate.m for multiple contrasts.
(3) Corrected cg_tfce_estimate for reduced designs, where contrast vector 
    does not comprises all subjects.

------------------------------------------------------------------------
r18 | gaser | 2010-07-28 16:34:33 +0200 (Wed, 28 Jul 2010) | 5 lines

Changed paths:
M      cg_tfce_estimate.m

Added checks for empty index of in cg_tfce_estimate.m

------------------------------------------------------------------------
r17 | gaser | 2010-07-26 09:08:30 +0200 (Mon, 26 Jul 2010) | 6 lines

Changed paths:
M      cg_tfce_list.m
M      cg_getTFCE.m

Considered spm8 updates 4010.

------------------------------------------------------------------------
r16 | gaser | 2010-07-23 17:21:52 +0200 (Fri, 23 Jul 2010) | 7 lines

Changed paths:
A      cg_glm_get_Beta_ResSS.mexmaci
A      cg_glm_get_Beta_ResSS.mexw64
A      tfceMex.mexmaci

Now really added mexmaci files.

------------------------------------------------------------------------
r15 | gaser | 2010-07-23 13:20:18 +0200 (Fri, 23 Jul 2010) | 8 lines

Changed paths:
M      Makefile.tfce
M      tfceMex.m
A      make.m

(1) Added make.m for easier compilation.
(2) Added mexmaci files.

------------------------------------------------------------------------
r14 | gaser | 2010-07-23 12:43:49 +0200 (Fri, 23 Jul 2010) | 10 lines

Changed paths:
M      cg_tfce_list.m
D      spm_TFCE.m
A  +   spm_tfce.m
M      Makefile.tfce
M      cg_getTFCE.m

(1) Renamed spm_TFCE.m to spm_tfce.m.
(2) Added some additional information for result table in to cg_tfce_list.m.

------------------------------------------------------------------------
r13 | gaser | 2010-07-23 11:46:27 +0200 (Fri, 23 Jul 2010) | 11 lines

Changed paths:
M      Contents_info.txt
M      cg_glm_get_Beta_ResSS.mexmaci64
M      Makefile.tfce
M      Makefile

(1) Updated Contents_info.txt and Makefile.tfce to also mention SPM5.
(2) Changed Makefile to skip creation of an archives, which causes problems
    with Windows64.
(3) Added compilation for w64.

------------------------------------------------------------------------
r12 | gaser | 2010-07-22 18:00:32 +0200 (Thu, 22 Jul 2010) | 8 lines

Changed paths:
M       cg_glm_get_Beta_ResSS.c
A       cg_glm_get_Beta_ResSS.mexw32
A       tfceMex.mexw32

(1) Made cg_glm_get_Beta_ResSS.c conform to compile with w32.
(2) Added *.mexw32 

------------------------------------------------------------------------
r11 | gaser | 2010-07-22 17:11:11 +0200 (Thu, 22 Jul 2010) | 7 lines

Changed paths:
A      tfceMex.mexw64
M      cg_getTFCE.m

(1) Added tfceMex.mexw64.
(2) Added warning for FDR.

------------------------------------------------------------------------
r10 | gaser | 2010-07-22 16:32:17 +0200 (Thu, 22 Jul 2010) | 7 lines

Changed paths:
D      spm_vol_utils.mexmaci64.a
D      spm_vol_utils.mexa64.a
D      spm_vol_utils.mexglx.a

Removed *.a files.

------------------------------------------------------------------------
r9 | gaser | 2010-07-22 16:26:39 +0200 (Thu, 22 Jul 2010) | 17 lines

Changed paths:
D      tfce8.txt
A  +   spm_TFCE.m
M      Makefile.tfce
A  +   TFCE.txt
A      cg_glm_get_Beta_ResSS.mexglx
A      spm_vol_utils.mexmaci64.a
A      spm_vol_utils.mexglx.a
A      spm_vol_utils.mexa64.a
D      spm_tfce8.m
M      CHANGES.txt
A      tfceMex.mexglx
A      tfceMex.mexa64

(1) Renamed tfce8 to TFCE.
(2) Compiled for linux

------------------------------------------------------------------------
r8 | gaser | 2010-07-22 15:26:39 +0200 (Thu, 22 Jul 2010) | 14 lines

Changed paths:
M      cg_tfce_estimate.m
M      cg_tfce_list.m
D      tfce8.man
A      spm_tfce8.m
M      cg_getTFCE.m
A  +   tfce8.txt
M      Makefile.tfce
M      cg_tfce_results.m
M      Makefile

(1) Added spm_tfce8.m
(2) Many changes to get listing of p-values working.

------------------------------------------------------------------------
r7 | gaser | 2010-07-22 06:37:00 +0200 (Thu, 22 Jul 2010) | 8 lines

Changed paths:
A       cg_tfce_list.m
M       cg_tfce_estimate.m
M       CHANGES.txt
M       cg_tfce_results.m

Preliminary version for listing of results.

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r6 | gaser | 2010-07-21 18:20:30 +0200 (Wed, 21 Jul 2010) | 10 lines

Changed paths:
A  +   cg_tfce_estimate.m
A      cg_getTFCE.m
A      cg_tfce_results.m
D      cg_tfce8.m

(1) Added cg_tfce_results.m and cg_getTFCE.m for result presentation.
(2) Renamed cg_tfce8.m to cg_tfce_estimate.m.


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r5 | gaser | 2010-07-21 07:40:41 +0200 (Wed, 21 Jul 2010) | 5 lines

Changed paths:
M       cg_tfce8.m

New version with corrected p-maps.

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r4 | gaser | 2010-07-21 07:39:42 +0200 (Wed, 21 Jul 2010) | 6 lines

Changed paths:
A      CHANGES.txt

Added CHANGES.txt.


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r3 | gaser | 2010-07-20 18:18:42 +0200 (Tue, 20 Jul 2010) | 5 lines

Changed paths:
M      cg_tfce8.m

Added preliminary version for uncorrected p-values.

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r2 | gaser | 2010-07-20 15:12:14 +0200 (Tue, 20 Jul 2010) | 5 lines

Changed paths:
M      Makefile.tfce

Added cg_glm_get_Beta_ResSS.m tfceMex.m to Makefile.tfce.

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r1 | gaser | 2010-07-20 14:29:01 +0200 (Tue, 20 Jul 2010) | 1 line

Initial import
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