SPM8 r6313

@meeg/sconfounds.m

@@ -5,10 +5,10 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: sconfounds.m 4657 2012-02-16 17:15:38Z vladimir $
+% $Id: sconfounds.m 5569 2013-07-01 11:10:00Z vladimir $
 
 if nargin == 2
-    meegind = meegchannels(this);
+    meegind = meegchannels(this, 'MEEG');
 
     [sel1, sel2] = match_str(chanlabels(this, meegind), newsconfounds.label);
 

Contents.m

@@ -1,5 +1,5 @@
 % Statistical Parametric Mapping
-% Version 5236 (SPM8) 04-Feb-13
+% Version 6313 (SPM8) 23-Jan-2015
 %__________________________________________________________________________
 %  ___  ____  __  __
 % / __)(  _ \(  \/  )  
@@ -40,9 +40,9 @@
 % You should  have received a copy of the  GNU General Public License along
 % with SPM, in spm_LICENCE.man. If not, see <http://www.gnu.org/licenses/>.
 %__________________________________________________________________________
-% Copyright (C) 1991,1994-2013 Wellcome Trust Centre for Neuroimaging
+% Copyright (C) 1991,1994-2015 Wellcome Trust Centre for Neuroimaging
 
-% $Id: Contents.m 5232 2013-02-04 15:15:06Z guillaume $
+% $Id: Contents.m 6312 2015-01-23 13:01:57Z guillaume $
 
 %==========================================================================
 % PROGRAMMERS NOTE:

README.txt

@@ -48,7 +48,7 @@ See http://www.fil.ion.ucl.ac.uk/spm/software/spm8/ for details.
 Later versions of MATLAB (released after SPM8), will probably
 need additional patches in order to run.  Once developed, these will 
 be made available from:
-     ftp://ftp.fil.ion.ucl.ac.uk/spm/spm8_updates/ 
+     http://www.fil.ion.ucl.ac.uk/spm/download/spm8_updates/
 
 With the compiled c-mex files in place, simply prepend the SPM
 directory to your MATLAB path to complete the installation. (Type `help
@@ -109,4 +109,4 @@ ________________________________________________________________________
 SPM is developed by members and collaborators of the
                                   Wellcome Trust Centre for Neuroimaging
 
-$Id: README.txt 5187 2013-01-17 12:10:06Z guillaume $
+$Id: README.txt 5638 2013-09-17 17:39:18Z guillaume $

config/spm_cfg_eeg_inv_headmodel.m

@@ -5,7 +5,7 @@
 % Copyright (C) 2010 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: spm_cfg_eeg_inv_headmodel.m 4997 2012-10-12 11:17:08Z vladimir $
+% $Id: spm_cfg_eeg_inv_headmodel.m 5988 2014-05-15 12:24:42Z vladimir $
 
 D = cfg_files;
 D.tag = 'D';
@@ -168,6 +168,8 @@
 for i = 1:numel(job.D)
     D = spm_eeg_load(job.D{i});
 
+    [ok, D] = check(D, '3d');
+
     if ~isfield(D,'inv')
         val   = 1;
     elseif numel(D.inv)<job.val

external/Makefile

@@ -3,13 +3,12 @@
 #
 # Copyright (C) 2008-2012 Wellcome Trust Centre for Neuroimaging
 #
-# $Id: Makefile 5144 2012-12-20 16:20:49Z guillaume $
+# $Id: Makefile 6144 2014-09-01 16:55:31Z guillaume $
 
 include ../src/Makefile.var
 
 FIELDTRIPMEX =\
 	fieldtrip/src/read_24bit.$(SUF) fieldtrip/src/read_16bit.$(SUF) \
-	fieldtrip/src/mxSerialize.$(SUF) fieldtrip/src/mxDeserialize.$(SUF) \
 	fieldtrip/src/ft_getopt.$(SUF) \
 	\
 	fieldtrip/src/nanmean.$(SUF) fieldtrip/src/nannumel.$(SUF) \
@@ -38,8 +37,6 @@ distclean: clean bemcp-distclean
 
 install: bemcp-install
 	$(COPY) fieldtrip/src/read_24bit.$(SUF) fieldtrip/fileio/private/
-	$(COPY) fieldtrip/src/mxSerialize.$(SUF) fieldtrip/fileio/private/
-	$(COPY) fieldtrip/src/mxDeserialize.$(SUF) fieldtrip/fileio/private/
 	$(COPY) fieldtrip/src/read_16bit.$(SUF) fieldtrip/fileio/private/
 	$(COPY) fieldtrip/src/nanmean.$(SUF) fieldtrip/fileio/private/
 	$(COPY) fieldtrip/src/nannumel.$(SUF) fieldtrip/fileio/private/
@@ -68,15 +65,12 @@ install: bemcp-install
 	$(COPY) fieldtrip/src/nannumel.$(SUF) fieldtrip/private/
 	$(COPY) fieldtrip/src/nansum.$(SUF) fieldtrip/private/
 	$(COPY) fieldtrip/src/nanvar_base.$(SUF) fieldtrip/private/
-	$(COPY) fieldtrip/src/mxSerialize.$(SUF) fieldtrip/private/
-	$(COPY) fieldtrip/src/mxDeserialize.$(SUF) fieldtrip/private/
 
 	$(COPY) fieldtrip/src/ft_getopt.$(SUF) fieldtrip/utilities/
 	$(COPY) fieldtrip/src/nanmean.$(SUF) fieldtrip/utilities/private/
 	$(COPY) fieldtrip/src/nannumel.$(SUF) fieldtrip/utilities/private/
 	$(COPY) fieldtrip/src/nansum.$(SUF) fieldtrip/utilities/private/
 	$(COPY) fieldtrip/src/nanvar_base.$(SUF) fieldtrip/utilities/private/
-	$(COPY) fieldtrip/src/mxSerialize.$(SUF) fieldtrip/utilities/private/
 	$(COPY) fieldtrip/src/ptriproj.$(SUF) fieldtrip/utilities/private/
 	$(COPY) fieldtrip/src/lmoutr.$(SUF) fieldtrip/utilities/private/
 

external/fieldtrip/connectivity/private/nanmean.m

@@ -4,7 +4,7 @@
 
 
 function y = nanmean(x, dim)
-N = sum(~isnan(t), dim);
+N = sum(~isnan(x), dim);
 y = nansum(x, dim) ./ N;
 
-end
+end

external/fieldtrip/fileio/ft_read_event.m

@@ -293,14 +293,19 @@
     schan = find(strcmpi(hdr.label,'STATUS'));
     sdata = ft_read_data(filename, 'header', hdr, 'dataformat', dataformat, 'begsample', begsample, 'endsample', endsample, 'chanindx', schan);
 
-    % find indices of negative numbers
-    bit24i = find(sdata < 0);
-    % make number positive and preserve bits 0-22
-    sdata(bit24i) = bitcmp(abs(sdata(bit24i))-1,24);
-    % re-insert the sign bit on its original location, i.e. bit24
-    sdata(bit24i) = sdata(bit24i)+(2^(24-1));
-    % typecast the data to ensure that the status channel is represented in 32 bits
-    sdata = uint32(sdata);
+    try
+        % find indices of negative numbers
+        bit24i = find(sdata < 0);
+        % make number positive and preserve bits 0-22
+        sdata(bit24i) = bitcmp(abs(sdata(bit24i))-1,24);
+        % re-insert the sign bit on its original location, i.e. bit24
+        sdata(bit24i) = sdata(bit24i)+(2^(24-1));
+        % typecast the data to ensure that the status channel is represented in 32 bits
+        sdata = uint32(sdata);
+    catch
+        % convert to 32-bit integer representation and only preserve the lowest 24 bits
+        sdata = bitand(int32(sdata), 2^24-1);
+    end
 
     byte1 = 2^8  - 1;
     byte2 = 2^16 - 1 - byte1;

external/fieldtrip/fileio/private/nanmean.m

@@ -4,7 +4,7 @@
 
 
 function y = nanmean(x, dim)
-N = sum(~isnan(t), dim);
+N = sum(~isnan(x), dim);
 y = nansum(x, dim) ./ N;
 
-end
+end

external/fieldtrip/forward/private/triangle4pt.m

@@ -34,7 +34,7 @@
 % written by Christophe Phillips, 2009/01/19
 % Cyclotron Research Centre, University of li?ge, belgium
 %
-% $Id: triangle4pt.m 7123 2012-12-06 21:21:38Z roboos $
+% $Id: triangle4pt.m 8447 2013-09-05 17:48:57Z vlalit $
 
 Ns = length(vol.bnd);
 for ii=1:Ns % treat each mesh one at a time
@@ -53,7 +53,7 @@
     lt(lt==jj) = [];
     % list of 3 directly surrounding triangles
     lv = tri(lt,:);
-    lv = setxor(lv(:),tri(jj,:));
+    lv = setxor(lv(:)',tri(jj,:));
     % list of 3 voxels connected by 2 edges to the jj_th triangle.
     sph_pnt = pnt([tri(jj,:) lv],:);
     [center,radius] = fitsphere(sph_pnt);

external/fieldtrip/ft_defaults.m

@@ -51,11 +51,11 @@
 if ~isfield(ft_default, 'trackconfig'),    ft_default.trackconfig    = 'off';    end % cleanup, report, off
 if ~isfield(ft_default, 'checkconfig'),    ft_default.checkconfig    = 'loose';  end % pedantic, loose, silent
 if ~isfield(ft_default, 'checksize'),      ft_default.checksize      = 1e5;      end % number in bytes, can be inf
-if ~isfield(ft_default, 'showcallinfo'),   ft_default.showcallinfo   = 'yes';    end % yes or no, this is used in ft_pre/postamble_provenance
+if ~isfield(ft_default, 'showcallinfo'),   ft_default.showcallinfo   = 'no';    end % yes or no, this is used in ft_pre/postamble_provenance
 if ~isfield(ft_default, 'debug'),          ft_default.debug          = 'no';     end % no, save, saveonerror, display, displayonerror, this is used in ft_pre/postamble_debug
 
 % these options allow to disable parts of the provenance
-if ~isfield(ft_default, 'trackcallinfo'),  ft_default.trackcallinfo  = 'yes';    end % yes or no
+if ~isfield(ft_default, 'trackcallinfo'),  ft_default.trackcallinfo  = 'no';    end % yes or no
 if ~isfield(ft_default, 'trackdatainfo'),  ft_default.trackdatainfo  = 'no';     end % yes or no, this is still under development
 if ~isfield(ft_default, 'trackparaminfo'), ft_default.trackparaminfo = 'no';     end % yes or no, this is still under development
 

external/fieldtrip/private/nanmean.m

@@ -4,7 +4,7 @@
 
 
 function y = nanmean(x, dim)
-N = sum(~isnan(t), dim);
+N = sum(~isnan(x), dim);
 y = nansum(x, dim) ./ N;
 
-end
+end

external/fieldtrip/private/triangle4pt.m

@@ -34,7 +34,7 @@
 % written by Christophe Phillips, 2009/01/19
 % Cyclotron Research Centre, University of li?ge, belgium
 %
-% $Id: triangle4pt.m 7123 2012-12-06 21:21:38Z roboos $
+% $Id: triangle4pt.m 8447 2013-09-05 17:48:57Z vlalit $
 
 Ns = length(vol.bnd);
 for ii=1:Ns % treat each mesh one at a time
@@ -53,7 +53,7 @@
     lt(lt==jj) = [];
     % list of 3 directly surrounding triangles
     lv = tri(lt,:);
-    lv = setxor(lv(:),tri(jj,:));
+    lv = setxor(lv(:)',tri(jj,:));
     % list of 3 voxels connected by 2 edges to the jj_th triangle.
     sph_pnt = pnt([tri(jj,:) lv],:);
     [center,radius] = fitsphere(sph_pnt);

external/fieldtrip/src/nanmean.m

@@ -4,7 +4,7 @@
 
 
 function y = nanmean(x, dim)
-N = sum(~isnan(t), dim);
+N = sum(~isnan(x), dim);
 y = nansum(x, dim) ./ N;
 
-end
+end

external/fieldtrip/statfun/private/nanmean.m

@@ -4,7 +4,7 @@
 
 
 function y = nanmean(x, dim)
-N = sum(~isnan(t), dim);
+N = sum(~isnan(x), dim);
 y = nansum(x, dim) ./ N;
 
-end
+end

external/fieldtrip/utilities/private/nanmean.m

@@ -4,7 +4,7 @@
 
 
 function y = nanmean(x, dim)
-N = sum(~isnan(t), dim);
+N = sum(~isnan(x), dim);
 y = nansum(x, dim) ./ N;
 
-end
+end

man/meeg/eeg_imaging.tex

@@ -90,7 +90,7 @@ \section{Forward computation (\textit{forward})}
 
 
 \section{Inverse reconstruction}
-To get started press the \texttt{Invert} button. The first choice you will see is between \texttt{Imaging}, \texttt{VB-ECD} and \texttt{Beamforming}. For reconstruction based on an empirical Bayesian approach to localize either the evoked response, the evoked power or the induced power, as measured by EEG or MEG press the \texttt{Imaging} button. The other options are explained in greater detail elsewhere.
+To get started press the \texttt{Invert} button. The first choice you will see is between \texttt{Imaging}, \texttt{VB-ECD} and \texttt{DCM}. For reconstruction based on an empirical Bayesian approach to localize either the evoked response, the evoked power or the induced power, as measured by EEG or MEG press the \texttt{Imaging} button. The other options are explained in greater detail elsewhere.
 
 If you have trials belonging to more than one condition in your dataset then the next choice you will have is whether to invert all the conditions together or to choose a subset. It is recommended to invert the conditions together if you are planning to later do a statistical comparison between them. If you have only one condition, or after choosing the conditions, you will get a choice between ``Standard'' and ``Custom'' inversion. If you choose ``Standard'' inversion, SPM will start the computation with default settings. These correspond to the multiple sparse priors (MSP) algorithm \cite{karl_msp} which is then applied to the whole input data segment.
 

matlabbatch/cfg_getfile.m

@@ -85,7 +85,7 @@
 % Copyright (C) 2007 Freiburg Brain Imaging
 
 % John Ashburner and Volkmar Glauche
-% $Id: cfg_getfile.m 4863 2012-08-27 08:09:23Z volkmar $
+% $Id: cfg_getfile.m 6251 2014-10-30 13:58:44Z volkmar $
 
 t = {};
 sts = false;
@@ -364,7 +364,7 @@
     'units','normalized',...
     'Position',posinpanel([0.05+3*cw .5 0.45-3*cw .45],pcntp),...
     bf,...
-    'Callback',@delete,...
+    'Callback',@(h,e)delete(h),...
     'tag','D',...
     'ForegroundColor',col3,...
     'BackgroundColor',col1,...
@@ -395,7 +395,7 @@
     'ForegroundColor',col3,...
     'BackgroundColor',col1,...
     lf,...
-    'Callback',@update,...
+    'Callback',@(ob,ev)update(ob),...
     'tag','regexp',...
     'String',filt,...
     'UserData',sfilt);
@@ -756,7 +756,7 @@ function click_dir_box(lb,varargin)
 %=======================================================================
 function update(lb,dr)
 lb = sib(lb,'dirs');
-if nargin<2 || isempty(dr),
+if nargin<2 || isempty(dr) || ~ischar(dr)
     dr = get(lb,'UserData');
 end;
 if ~(strcmpi(computer,'PCWIN') || strcmpi(computer,'PCWIN64'))
@@ -1232,7 +1232,7 @@ function editeval(ob,varargin)
 ob  = sib(ob, 'EditWindow');
 str = get(ob, 'String');
 if ~isempty(str)
-    [out sts] = cfg_eval_valedit(char(str));
+    [out,sts] = cfg_eval_valedit(char(str));
     if sts && (iscellstr(out) || ischar(out))
         set(ob, 'String', cellstr(out));
     else
@@ -1248,7 +1248,7 @@ function editeval(ob,varargin)
 function editdone(ob,varargin)
 ob  = get(ob,'Parent');
 ob  = sib(ob,'EditWindow');
-str = get(ob,'String');
+str = cellstr(get(ob,'String'));
 if isempty(str) || isempty(str{1})
     str = {};
 else
@@ -1266,9 +1266,9 @@ function editdone(ob,varargin)
     end
     filt = getfilt(ob);
     if filt.code >= 0 % filter files, but not dirs
-        [p n e] = cellfun(@fileparts, str, 'uniformoutput',false);
+        [p,n,e] = cellfun(@fileparts, str, 'uniformoutput',false);
         fstr = strcat(n, e);
-        [fstr1 fsel] = do_filter(fstr, filt.ext);
+        [fstr1,fsel] = do_filter(fstr, filt.ext);
         str = str(fsel);
     end
 end

matlabbatch/cfg_ui.m

@@ -27,9 +27,9 @@
 % Copyright (C) 2007 Freiburg Brain Imaging
 
 % Volkmar Glauche
-% $Id: cfg_ui.m 4863 2012-08-27 08:09:23Z volkmar $
+% $Id: cfg_ui.m 6128 2014-08-01 16:09:57Z guillaume $
 
-rev = '$Rev: 4863 $'; %#ok
+rev = '$Rev: 6128 $'; %#ok
 
 % edit the above text to modify the response to help cfg_ui
 
@@ -693,8 +693,7 @@ function local_valedit_edit(hObject)
         ' ', ...
         'To clear a value, enter an empty cell ''{}''.', ...
         ' ', ...
-        ['Accept input with CTRL-RETURN, cancel with ' ...
-        'ESC.']});
+        'Leave input box with CTRL-TAB to access buttons.'});
     failtxt = {'Input could not be evaluated. Possible reasons are:',...
         '1) Input should be a vector or matrix, but is not enclosed in ''['' and '']'' brackets.',...
         '2) Input should be a character or string, but is not enclosed in '' single quotes.',...
@@ -716,8 +715,7 @@ function local_valedit_edit(hObject)
         ' ', ...
         'To clear a value, clear the input field and accept.', ...
         ' ', ...
-        ['Accept input with CTRL-RETURN, cancel with ' ...
-        'ESC.']});
+        'Leave input box with CTRL-TAB to access buttons.'});
     failtxt = {'Input could not be evaluated.'};
 end
 sts = false;

matlabbatch/gencode_rvalue.m

@@ -25,9 +25,9 @@
 % Copyright (C) 2007 Freiburg Brain Imaging
 
 % Volkmar Glauche
-% $Id: gencode_rvalue.m 4864 2012-08-27 13:57:31Z volkmar $
+% $Id: gencode_rvalue.m 6128 2014-08-01 16:09:57Z guillaume $
 
-rev = '$Rev: 4864 $'; %#ok
+rev = '$Rev: 6128 $'; %#ok
 
 str = {};
 sts = true;
@@ -109,8 +109,17 @@
                 else
                     sitem = mat2str(item,'class');
                 end
-                bsz   = max(numel(sitem)+2,100); % bsz needs to be > 100 and larger than string length
-                str1 = textscan(sitem, '%s', 'delimiter',';', 'bufsize',bsz); 
+                try
+                    if ~verLessThan('matlab', '8.4')
+                        bszopt = {};
+                    else
+                        error('Need bufsize option');
+                    end
+                catch
+                    bsz   = max(numel(sitem)+2,100); % bsz needs to be > 100 and larger than string length
+                    bszopt = {'bufsize', bsz};
+                end
+                str1 = textscan(sitem, '%s', 'delimiter',';', bszopt{:});
                 if numel(str1{1}) > 1
                     str = str1{1};
                 else