Maintenance: remove SVN keywords and update copyright

SVN r8278
spm · Jul 7, 2022 · 9564a81 · 9564a81
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diff --git a/Contents.m b/Contents.m
@@ -37,7  37,6 @@
 %__________________________________________________________________________
 % Copyright (C) 1991,1994-2022 Wellcome Centre for Human Neuroimaging
 
-% $Id: Contents.m 8208 2022-01-12 11:10:09Z spm $
 
 %==========================================================================
 % PROGRAMMERS NOTE:

diff --git a/LICENCE.txt b/LICENCE.txt
@@ -356,4  356,3 @@
 % Copyright (C) 1991,1994-2022 Wellcome Centre for Human Neuroimaging
 
 % The FIL Methods Group
-% $Id: LICENCE.txt 8208 2022-01-12 11:10:09Z spm $
diff --git a/README.md b/README.md
@@ -120,5  120,4 @@ supplied as is.  No formal support or maintenance is provided or implied.
 
 ```
 Copyright (C) 1991,1994-2022 Wellcome Centre for Human Neuroimaging
-$Id: README.md 8208 2022-01-12 11:10:09Z spm $
 ```
diff --git a/batches/preproc_fmri.m b/batches/preproc_fmri.m
@@ -17,10  17,9 @@
 % have multiple structurals in one directory, you will need to replace
 % "brain" with a unique filename for each subject.
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: preproc_fmri.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('preproc_fmri', 'file') && ~isdeployed
     help preproc_fmri

diff --git a/batches/preproc_fmri_simplified.m b/batches/preproc_fmri_simplified.m
@@ -6,10  6,9 @@
 %   module of the created batch)
 % * The structural image volume (in the "Segment" module)
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: preproc_fmri_simplified.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('preproc_fmri_simplified', 'file') && ~isdeployed
     help preproc_fmri_simplified

diff --git a/batches/preproc_fmri_without_anat.m b/batches/preproc_fmri_without_anat.m
@@ -9,10  9,9 @@
 % * The slice timing acquisition details (if you're unsure, don't use STC!)
 % * The functional images for each session (only in the first module)
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: preproc_fmri_without_anat.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('preproc_fmri_without_anat', 'file') && ~isdeployed
     help preproc_fmri_without_anat

diff --git a/batches/preproc_vbm.m b/batches/preproc_vbm.m
@@ -10,10  10,9 @@
 % be left in the directory of the first selected structural image; not
 % moved to the Templates_etc directory along with the Template image files.
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: preproc_vbm.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('preproc_vbm', 'file') && ~isdeployed
     help preproc_vbm

diff --git a/batches/preproc_vbm_simplified.m b/batches/preproc_vbm_simplified.m
@@ -3,10  3,9 @@
 % Need to specify:
 % * Structural images for all subjects
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: preproc_vbm_simplified.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('preproc_vbm_simplified', 'file') && ~isdeployed
     help preproc_vbm_simplified

diff --git a/batches/stats1_within_subject_fmri.m b/batches/stats1_within_subject_fmri.m
@@ -11,10  11,9 @@
 % * Conditions (not needed for resting-state studies)
 % * Multiple regressors - the realignment parameters from motion correction
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: stats1_within_subject_fmri.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('stats1_within_subject_fmri', 'file') && ~isdeployed
     help stats1_within_subject_fmri

diff --git a/batches/stats2_between_subject.m b/batches/stats2_between_subject.m
@@ -9,10  9,9 @@
 % * The details of your design (!)
 % * An explicit mask (for VBM)
 %__________________________________________________________________________
-% Copyright (C) 2014 Wellcome Trust Centre for Neuroimaging
 
 % Ged Ridgway
-% $Id: stats2_between_subject.m 6177 2014-09-16 10:44:55Z guillaume $
 % Copyright (C) 2014-2022 Wellcome Centre for Human Neuroimaging
 
 if exist('stats2_between_subject', 'file') && ~isdeployed
     help stats2_between_subject

diff --git a/bin/spm12-matlab b/bin/spm12-matlab
@@ -3,10  3,8 @@
 # Command Line Interface for SPM
 # SPM: https://www.fil.ion.ucl.ac.uk/spm/
 #
-# Copyright (C) 2017-2021 Wellcome Centre for Human Neuroimaging
-#
 # Guillaume Flandin
-# $Id: spm12-matlab 8167 2021-10-15 16:56:11Z guillaume $ 
 # Copyright (C) 2017-2022 Wellcome Centre for Human Neuroimaging
 
 PLATFORM=$(uname)
 

diff --git a/bin/spm12-mcr b/bin/spm12-mcr
@@ -1,12  1,10 @@
 #!/bin/sh
 #
 # Command Line Interface for SPM
-# SPM: http://www.fil.ion.ucl.ac.uk/spm/
-#
-# Copyright (C) 2017 Wellcome Trust Centre for Neuroimaging
 # SPM: https://www.fil.ion.ucl.ac.uk/spm/
 #
 # Guillaume Flandin
-# $Id: spm12-mcr 7014 2017-02-13 12:31:33Z guillaume $ 
 # Copyright (C) 2017-2022 Wellcome Centre for Human Neuroimaging
 
 if [ "${MCR_HOME}" = "" ]; then
   echo "Set MCR_HOME environment variable." >&2 

diff --git a/bin/spm12-octave b/bin/spm12-octave
@@ -1,12  1,10 @@
 #!/usr/bin/octave -fqH
 #
 # Command Line Interface for SPM
-# SPM: http://www.fil.ion.ucl.ac.uk/spm/
-#
-# Copyright (C) 2017 Wellcome Trust Centre for Neuroimaging
 # SPM: https://www.fil.ion.ucl.ac.uk/spm/
 #
 # Guillaume Flandin
-# $Id: spm12-octave 7284 2018-03-29 09:42:26Z guillaume $ 
 # Copyright (C) 2017-2022 Wellcome Centre for Human Neuroimaging
 
 
 spm_dir = getenv ("SPM_HOME");

diff --git a/canonical/spm_mesh.man b/canonical/spm_mesh.man
@@ -46,7  46,6 @@
 % activations in spm using a macroscopic anatomical parcellation of the MNI 
 % MRI single subject brain. Neuroimage 15, 273-289.
 %__________________________________________________________________________
-% Copyright (C) 2009-2012 Wellcome Trust Centre for Neuroimaging
 
 % Rik Henson, Daniel Wakeman and John Ashburner
-% $Id: spm_mesh.man 5039 2012-11-06 20:39:58Z guillaume $
 % Copyright (C) 2009-2022 Wellcome Centre for Human Neuroimaging
diff --git a/spm.m b/spm.m
@@ -50,10  50,9 @@
 % FORMAT & help in the main body of spm.m
 %
 %_______________________________________________________________________
-% Copyright (C) 1991,1994-2022 Wellcome Centre for Human Neuroimaging
 
 % Andrew Holmes
-% $Id: spm.m 8216 2022-02-01 17:56:49Z guillaume $
 % Copyright (C) 1991,1994-2022 Wellcome Centre for Human Neuroimaging
 
 
 %=======================================================================

diff --git a/spm_ADEM.m b/spm_ADEM.m
@@ -1,6  1,6 @@
-function [DEM] = spm_ADEM(DEM)
 function DEM = spm_ADEM(DEM)
 % Dynamic expectation maximisation:  Active inversion
-% FORMAT DEM   = spm_ADEM(DEM)
 % FORMAT DEM = spm_ADEM(DEM)
 %
 % DEM.G  - generative process
 % DEM.M  - recognition  model
@@ -129,13  129,12 @@
 % in generalised coordinates.  This means DEM can deconvolve online and 
 % represents an alternative to Kalman filtering or alternative Bayesian
 % update procedures.
-%
 %__________________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_ADEM.m 8183 2021-11-04 15:25:19Z guillaume $
-
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 % check model, data, priors and unpack
 %--------------------------------------------------------------------------
 DEM   = spm_ADEM_set(DEM);

diff --git a/spm_ADEM_M_set.m b/spm_ADEM_M_set.m
@@ -1,6  1,6 @@
-function [M] = spm_ADEM_M_set(M)
 function M = spm_ADEM_M_set(M)
 % Set indices and perform checks on hierarchical action models
-% FORMAT [M] = spm_ADEM_M_set(M)
 % FORMAT M = spm_ADEM_M_set(M)
 %
 % for each level (i); required fields
 %
@@ -40,10  40,9 @@
 % If the highest level involves any dynamic or static transformation
 % of its inputs a further level is added with flat priors
 %__________________________________________________________________________
-% Copyright (C) 2008-2014 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_ADEM_M_set.m 5962 2014-04-17 12:47:43Z spm $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 % order

diff --git a/spm_ADEM_diff.m b/spm_ADEM_diff.m
@@ -1,6  1,6 @@
 function [u,dg,df] = spm_ADEM_diff(M,u)
 % Evaluate an active model given innovations z{i} and w{i}
-% FORMAT [u dg df] = spm_ADEM_diff(M,u);
 % FORMAT [u,dg,df] = spm_ADEM_diff(M,u)
 %
 % M    - generative model
 %
@@ -14,10  14,9 @@
 %
 % The system is evaluated at the prior expectation of the parameters.
 %__________________________________________________________________________
-% Copyright (C) 2008-2014 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_ADEM_diff.m 5962 2014-04-17 12:47:43Z spm $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 % number of states and parameters

diff --git a/spm_ADEM_set.m b/spm_ADEM_set.m
@@ -1,16  1,15 @@
-function [DEM] = spm_ADEM_set(DEM)
 function DEM = spm_ADEM_set(DEM)
 % Perform checks on DEM structures for active inversion
-% FORMAT [DEM] = spm_ADEM_set(DEM)
 % FORMAT DEM = spm_ADEM_set(DEM)
 %
 % DEM.G  - generative model
 % DEM.M  - recognition model
 % DEM.C  - exogenous causes
 % DEM.U  - prior expectation of causes
 %__________________________________________________________________________
-% Copyright (C) 2008-2014 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_ADEM_set.m 5962 2014-04-17 12:47:43Z spm $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 % check recognition model

diff --git a/spm_ADEM_update.m b/spm_ADEM_update.m
@@ -1,6  1,6 @@
-function [DEM] = spm_ADEM_update(DEM,COV)
-% Updates ADEM structure using conditional expectations
-% FORMAT [DEM] = spm_ADEM_update(DEM,COV)
 function DEM = spm_ADEM_update(DEM,COV)
 % Update ADEM structure using conditional expectations
 % FORMAT DEM = spm_ADEM_update(DEM,COV)
 %
 % DEM - DEM structure
 % COV - Covariance of parameter (P) fluctuations (E): P(i   1) = P(i)   E
@@ -12,10  12,9 @@
 % called with an extra argument, the posterior variances of the
 % parameters are also updated.
 %__________________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_ADEM_update.m 6506 2015-07-24 10:26:51Z karl $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 % preliminaries

diff --git a/spm_ALAP.m b/spm_ALAP.m
@@ -1,6  1,6 @@
-function [DEM] = spm_ALAP(DEM)
 function DEM = spm_ALAP(DEM)
 % Laplacian model inversion (see also spm_LAP) with action
-% FORMAT DEM   = spm_ALAP(DEM)
 % FORMAT DEM = spm_ALAP(DEM)
 %
 % DEM.G  - generative process
 % DEM.M  - recognition  model
@@ -146,10  146,9 @@
 % This enables active inference (c.f., action-perception) or embodied
 % inference.
 %__________________________________________________________________________
-% Copyright (C) 2012 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_ALAP.m 8183 2021-11-04 15:25:19Z guillaume $
 % Copyright (C) 2012-2022 Wellcome Centre for Human Neuroimaging
 
 
 % check model, data and priors

diff --git a/spm_A_reduce.m b/spm_A_reduce.m
@@ -1,6  1,6 @@
 function [J,z,v,s] = spm_A_reduce(J,x,T,N)
 % Reduction of Markovian partition
 % FORMAT [J,z,v,s] = spm_A_reduce(J,x,T,N)
-% reduction of Markovian partition
 % J  - Jacobian (x)
 % x  - {3 x n}  particular partition of states
 % T  - eigenvalue threshold to retain eigenvectors [default: 8]
@@ -13,10  13,10 @@
 %
 % Adiabatic reduction operator (R)
 %__________________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Karl Friston
-% $Id: spm_A_reduce.m 8183 2021-11-04 15:25:19Z guillaume $
 % Copyright (C) 2019-2022 Wellcome Centre for Human Neuroimaging
 
 
 % preliminaries
 %--------------------------------------------------------------------------

diff --git a/spm_BIDS.m b/spm_BIDS.m
@@ -16,10  16,9 @@
 %   describing outputs of neuroimaging experiments.
 %   K. J. Gorgolewski et al, Scientific Data, 2016.
 %__________________________________________________________________________
-% Copyright (C) 2016-2018 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: spm_BIDS.m 8183 2021-11-04 15:25:19Z guillaume $
 % Copyright (C) 2016-2022 Wellcome Centre for Human Neuroimaging
 
 
 %-Validate input arguments

diff --git a/spm_BMS.m b/spm_BMS.m
@@ -30,10  30,10 @@
 % Bayesian model selection for group studies - Revisited. 
 % NeuroImage 84:971-85. doi: 10.1016/j.neuroimage.2013.08.065
 %__________________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Klaas Enno Stephan, Will Penny
-% $Id: spm_BMS.m 7679 2019-10-24 15:54:07Z spm $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 if nargin < 2 || isempty(Nsamp)
     Nsamp = 1e6;

diff --git a/spm_BMS_F.m b/spm_BMS_F.m
@@ -15,10  15,9 @@
 % Stephan KE, Penny WD, Daunizeau J, Moran RJ, Friston KJ
 % Bayesian Model Selection for Group Studies. Neuroimage 2009 46(4):1004-17
 %__________________________________________________________________________
-% Copyright (C) 2008-2021 Wellcome Centre for Human Neuroimaging
 
 % Will Penny
-% $Id: spm_BMS_F.m 8160 2021-10-01 09:42:13Z guillaume $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 alpha0 = sort(alpha0);

diff --git a/spm_BMS_F_smpl.m b/spm_BMS_F_smpl.m
@@ -8,10  8,9 @@
 % Stephan KE, Penny WD, Daunizeau J, Moran RJ, Friston KJ
 % Bayesian Model Selection for Group Studies. Neuroimage 2009 46(4):1004-17
 %__________________________________________________________________________
-% Copyright (C) 2008-2021 Wellcome Centre for Human Neuroimaging
 
 % Will Penny
-% $Id: spm_BMS_F_smpl.m 8160 2021-10-01 09:42:13Z guillaume $
 % Copyright (C) 2008-2022 Wellcome Centre for Human Neuroimaging
 
 
 % prevent numerical problems 

diff --git a/spm_BMS_bor.m b/spm_BMS_bor.m
@@ -15,10  15,9 @@
 % Bayesian model selection for group studies - Revisited. 
 % NeuroImage 84:971-85. doi: 10.1016/j.neuroimage.2013.08.065
 %__________________________________________________________________________
-% Copyright (C) 2015 Wellcome Trust Centre for Neuroimaging
 
 % Will Penny
-% $Id: spm_BMS_bor.m 6444 2015-05-21 11:15:48Z guillaume $
 % Copyright (C) 2015-2022 Wellcome Centre for Human Neuroimaging
 
 
 if nargin < 4

diff --git a/spm_BMS_gibbs.m b/spm_BMS_gibbs.m
@@ -16,10  16,9 @@
 % g_post   - [Ni x Nk] matrix of posterior probabilities with 
 %            g_post(i,k) being post prob that subj i used model k
 %__________________________________________________________________________
-% Copyright (C) 2009-2013 Wellcome Trust Centre for Neuroimaging
 
 % Will Penny
-% $Id: spm_BMS_gibbs.m 6381 2015-03-17 17:55:09Z will $
 % Copyright (C) 2009-2022 Wellcome Centre for Human Neuroimaging
 
 
 if nargin < 3 || isempty(Nsamp)