SPM8 r3164

@gifti/export.m

@@ -8,7 +8,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: export.m 2587 2009-01-05 12:11:39Z vladimir $
+% $Id: export.m 3081 2009-04-22 20:15:38Z guillaume $
 
 if numel(this) > 1, warning('Only handle scalar objects yet.'); end
 
@@ -18,6 +18,18 @@
     case 'matlab'
         s = struct(this);
 
+    case 'patch'
+        if isfield(this,'vertices')
+            s.vertices = subsref(this, substruct('.', 'vertices'));
+        end
+        if isfield(this,'faces')
+            s.faces = subsref(this, substruct('.', 'faces'));
+        end
+        if isfield(this,'cdata')  
+            s.facevertexcdata = subsref(this, substruct('.', 'cdata'));
+        end
+        try, s; catch, s = struct([]); end
+
     case {'fieldtrip', 'ft'}
         s = struct('tri',[], 'pnt',[]);
         if isfield(this,'vertices')
@@ -32,7 +44,7 @@
         if isfield(this,'vertices')
             s.vert = double(subsref(this, substruct('.', 'vertices')));
         end
-        if   isfield(this,'faces')  
+        if isfield(this,'faces')
             s.face = uint16(subsref(this, substruct('.', 'faces')));
         end
 

@meeg/condlist.m

@@ -6,7 +6,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: condlist.m 2877 2009-03-13 15:56:08Z vladimir $
+% $Id: condlist.m 3046 2009-04-02 14:28:31Z vladimir $
 
 res = getset(this, 'trials', 'label');
 if ~iscell(res)
@@ -24,7 +24,7 @@
     if numel(res)>1 && isfield(this.other, 'condlist') &&...
             iscell(this.other.condlist) && ~isempty(this.other.condlist)
         [sel1, sel2] = spm_match_str(this.other.condlist, res);
-        res = res([sel2 setdiff(1:numel(res), sel2)]);
+        res = res([sel2(:)' setdiff(1:numel(res), sel2)]);
     end
 else
     if iscell(newcondlist) && ~isempty(intersect(newcondlist, res))     

@meeg/pickconditions.m

@@ -8,16 +8,20 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel
-% $Id: pickconditions.m 2448 2008-11-07 16:56:07Z vladimir $
+% $Id: pickconditions.m 3146 2009-05-26 09:54:23Z vladimir $
 
 if nargin<3
     rejectbad = 1;
 end
 
 c = conditions(this);
 
-res = strmatch(deblank(label), deblank(c), 'exact');
-
+if isa(label, 'char')
+    label = {label};
+end
+
+res = find(ismember(c, label));
+
 if rejectbad && ~isempty(res)
     res = res(~reject(this, res));
 end

@meeg/private/checkmeeg.m

@@ -9,7 +9,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: checkmeeg.m 2978 2009-03-27 14:43:08Z guillaume $
+% $Id: checkmeeg.m 3068 2009-04-20 17:21:57Z vladimir $
 
 if nargin==1
     option = 'basic';
@@ -255,6 +255,17 @@
 
 if ~isfield(meegstruct, 'sensors')
     meegstruct.sensors = struct([]);
+else
+    if isfield(meegstruct.sensors, 'eeg')
+        if isempty(meegstruct.sensors.eeg) || isempty(meegstruct.sensors.eeg.pnt)
+            meegstruct.sensors = rmfield(meegstruct.sensors, 'eeg');
+        end
+    end
+    if isfield(meegstruct.sensors, 'meg')
+        if isempty(meegstruct.sensors.meg) || isempty(meegstruct.sensors.meg.pnt)
+            meegstruct.sensors = rmfield(meegstruct.sensors, 'meg');
+        end
+    end
 end
 
 if ~isfield(meegstruct, 'fiducials')

@nifti/private/decode_qform0.m

@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 %
-% $Id: decode_qform0.m 1143 2008-02-07 19:33:33Z spm $
+% $Id: decode_qform0.m 3131 2009-05-18 15:54:10Z guillaume $
 
 
 dim    = double(hdr.dim);
@@ -15,9 +15,9 @@
     %disp('The images are in a form whereby it is not possible to');
     %disp('tell the left and right sides of the brain apart.');
     %if flp,
-    %    disp('They are assumed to be stored right-handed.');
-    %else
     %    disp('They are assumed to be stored left-handed.');
+    %else
+    %    disp('They are assumed to be stored right-handed.');
     %end;
     %disp('------------------------------------------------------');
 

Contents.m

@@ -1,5 +1,5 @@
 % Statistical Parametric Mapping
-% Version 3042 (SPM8) 02-Apr-2009
+% Version 3164 (SPM8) 29-May-09
 %__________________________________________________________________________
 %  ___  ____  __  __
 % / __)(  _ \(  \/  )  
@@ -11,7 +11,7 @@
 %
 % SPM8 is written for MATLAB 7.1 (R14SP3) onwards under Windows and Unix.
 % ( Compiled binaries of external C-MEX functions are provided for:       )
-% (    Windows (32 and 64 bit), Linux (32 and 64 bit) and Mac (32 bit)    )
+% ( Windows (32 and 64 bit), Linux (32 and 64 bit) and Mac (32 and 64 bit))
 %
 % See spm.man for details of this release.
 % See README.txt for information on installation and getting started.
@@ -42,7 +42,7 @@
 %__________________________________________________________________________
 % Copyright (C) 1991,1994-2003,2005-2009 Wellcome Trust Centre for Neuroimaging
 
-% $Id: Contents.m 3041 2009-04-02 10:14:17Z guillaume $
+% $Id: Contents.m 3163 2009-05-29 14:04:55Z guillaume $
 
 %==========================================================================
 % PROGRAMMERS NOTE:

config/spm_cfg_eeg_convert.m

@@ -4,7 +4,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel
-% $Id: spm_cfg_eeg_convert.m 2720 2009-02-09 19:50:46Z vladimir $
+% $Id: spm_cfg_eeg_convert.m 3059 2009-04-15 18:09:13Z guillaume $
 
 dataset = cfg_files;
 dataset.tag = 'dataset';
@@ -207,8 +207,8 @@
 
         S.usetrials = 0;
         [S.trl, S.conditionlabel] = spm_eeg_definetrial(S);
-
     end
+    S.continuous = 0;
 end
 
 if isfield(S.channels, 'chanmeg')

config/spm_cfg_eeg_tf_rescale.m

@@ -0,0 +1,30 @@
+function S = spm_cfg_eeg_tf_rescale
+% configuration file for rescaling spectrograms
+%_______________________________________________________________________
+% Copyright (C) 2009 Wellcome Trust Centre for Neuroimaging
+
+% Will Penny
+% $Id: spm_cfg_eeg_tf_rescale.m 3090 2009-04-29 17:30:05Z will $
+
+Fname = cfg_files;
+Fname.tag = 'Fname';
+Fname.name = 'File Names';
+Fname.filter = 'mat';
+Fname.num = [1 inf];
+Fname.help = {'Select the M/EEG mat file.'};
+
+
+S = cfg_exbranch;
+S.tag = 'eeg_tf_rescale';
+S.name = 'M/EEG TF Rescale';
+S.val = {Fname};
+S.help = {'Rescale spectrogram using eg Log Ratio operator'};
+S.prog = @eeg_tf_rescale;
+S.modality = {'EEG'};
+
+
+function out = eeg_tf_rescale(job)
+% construct the S struct
+S = job;
+S.Fname = strvcat(job.Fname);
+

config/spm_cfg_factorial_design.m

@@ -1,12 +1,11 @@
 function factorial_design = spm_cfg_factorial_design
-% SPM Configuration file
-% automatically generated by the MATLABBATCH utility function GENCODE
+% SPM Configuration file for 2nd-level models
 %_______________________________________________________________________
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
-% $Id: spm_cfg_factorial_design.m 2975 2009-03-26 21:43:31Z guillaume $
+% Will Penny
+% $Id: spm_cfg_factorial_design.m 3067 2009-04-20 13:58:07Z guillaume $
 
-rev = '$Rev: 2975 $';
 % ---------------------------------------------------------------------
 % dir Directory
 % ---------------------------------------------------------------------
@@ -17,6 +16,7 @@
 dir.filter = 'dir';
 dir.ufilter = '.*';
 dir.num     = [1 1];
+
 % ---------------------------------------------------------------------
 % scans Scans
 % ---------------------------------------------------------------------
@@ -35,6 +35,7 @@
 t1.name    = 'One-sample t-test';
 t1.val     = {scans };
 t1.help    = {''};
+
 % ---------------------------------------------------------------------
 % scans1 Group 1 scans
 % ---------------------------------------------------------------------
@@ -144,6 +145,7 @@
 t2.name    = 'Two-sample t-test';
 t2.val     = {scans1 scans2 dept variance gmsca ancova };
 t2.help    = {''};
+
 % ---------------------------------------------------------------------
 % scans Scans [1,2]
 % ---------------------------------------------------------------------
@@ -168,20 +170,18 @@
 generic         = cfg_repeat;
 generic.tag     = 'generic';
 generic.name    = 'Pairs';
-generic.help    = {
-                   ''
-                   ''
-}';
-generic.values  = {pair };
+generic.help    = {''};
+generic.values  = {pair};
 generic.num     = [1 Inf];
 % ---------------------------------------------------------------------
 % pt Paired t-test
 % ---------------------------------------------------------------------
 pt         = cfg_branch;
 pt.tag     = 'pt';
 pt.name    = 'Paired t-test';
-pt.val     = {generic dept variance gmsca ancova };
+pt.val     = {generic gmsca ancova};
 pt.help    = {''};
+
 % ---------------------------------------------------------------------
 % scans Scans
 % ---------------------------------------------------------------------

config/spm_cfg_preproc.m

@@ -4,9 +4,9 @@
 %_______________________________________________________________________
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
-% $Id: spm_cfg_preproc.m 2834 2009-03-06 17:57:50Z john $
+% $Id: spm_cfg_preproc.m 3124 2009-05-18 08:13:52Z volkmar $
 
-rev = '$Rev: 2834 $';
+rev = '$Rev: 3124 $';
 % ---------------------------------------------------------------------
 % data Data
 % ---------------------------------------------------------------------
@@ -311,9 +311,6 @@
 %------------------------------------------------------------------------
 function dep = vout(job)
 opts  = job.output;
-% This depends on job contents, which may not be present when virtual
-% outputs are calculated.
-sopts = [opts.GM;opts.WM;opts.CSF];
 
 cdep(1)            = cfg_dep;
 cdep(1).sname      = 'Norm Params Subj->MNI';
@@ -329,25 +326,28 @@
     cdep(end).src_output = substruct('()',{1}, '.','biascorr','()',{':'});
     cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
 end;
+sonames = {'GM','WM','CSF'};
 for k1=1:3,
-    if sopts(k1,3),
-        cdep(end+1)          = cfg_dep;
-        cdep(end).sname      = sprintf('c%d Images',k1);
-        cdep(end).src_output = substruct('()',{1}, '.',sprintf('c%d',k1),'()',{':'});
-        cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
-    end;
-    if sopts(k1,2),
-        cdep(end+1)          = cfg_dep;
-        cdep(end).sname      = sprintf('wc%d Images',k1);
-        cdep(end).src_output = substruct('()',{1}, '.',sprintf('wc%d',k1),'()',{':'});
-        cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
-    end;
-    if sopts(k1,1),
-        cdep(end+1)          = cfg_dep;
-        cdep(end).sname      = sprintf('mwc%d Images',k1);
-        cdep(end).src_output = substruct('()',{1}, '.',sprintf('mwc%d',k1),'()',{':'});
-        cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
-    end;
+    if ~strcmp(opts.(sonames{k1}),'<UNDEFINED>')
+        if opts.(sonames{k1})(3),
+            cdep(end+1)          = cfg_dep;
+            cdep(end).sname      = sprintf('c%d Images',k1);
+            cdep(end).src_output = substruct('()',{1}, '.',sprintf('c%d',k1),'()',{':'});
+            cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
+        end;
+        if opts.(sonames{k1})(2),
+            cdep(end+1)          = cfg_dep;
+            cdep(end).sname      = sprintf('wc%d Images',k1);
+            cdep(end).src_output = substruct('()',{1}, '.',sprintf('wc%d',k1),'()',{':'});
+            cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
+        end;
+        if opts.(sonames{k1})(1),
+            cdep(end+1)          = cfg_dep;
+            cdep(end).sname      = sprintf('mwc%d Images',k1);
+            cdep(end).src_output = substruct('()',{1}, '.',sprintf('mwc%d',k1),'()',{':'});
+            cdep(end).tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
+        end;
+    end
 end;
 dep = cdep;
 

config/spm_cfg_reorient.m

@@ -4,9 +4,9 @@
 %_______________________________________________________________________
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
-% $Id: spm_cfg_reorient.m 1299 2008-04-03 08:55:09Z volkmar $
+% $Id: spm_cfg_reorient.m 3130 2009-05-18 14:41:31Z volkmar $
 
-rev = '$Rev: 1299 $';
+rev = '$Rev: 3130 $';
 % ---------------------------------------------------------------------
 % srcfiles Images to reorient
 % ---------------------------------------------------------------------
@@ -70,13 +70,33 @@
 transform.val     = {transM };
 transform.help    = {'Specify reorientation method.'};
 transform.values  = {transM transprm };
+% ---------------------------------------------------------------------
+% prefix Filename Prefix
+% ---------------------------------------------------------------------
+prefix         = cfg_entry;
+prefix.tag     = 'prefix';
+prefix.name    = 'Filename Prefix';
+prefix.help    = {['Specify the string to be prepended to the filenames ' ...
+                   'of the reoriented image file(s). If this is left ' ...
+                   'empty, the original files will be overwritten.']};
+prefix.strtype = 's';
+prefix.num     = [0 Inf];
+% This should not be hardcoded here
+prefix.val     = {''};
+% Final solution: defaults setting
+% prefix.def     = @(val)spm_get_defaults('reorient.prefix', val{:});
+% The following 3 lines should go into spm_defaults.m
+% % Reorient defaults
+% %=======================================================================
+% defaults.reorient.prefix = ''; % Output filename prefix ('' == overwrite)
+
 % ---------------------------------------------------------------------
 % reorient Reorient Images
 % ---------------------------------------------------------------------
 reorient         = cfg_exbranch;
 reorient.tag     = 'reorient';
 reorient.name    = 'Reorient Images';
-reorient.val     = {srcfiles transform };
+reorient.val     = {srcfiles transform prefix};
 reorient.help    = {'This facility allows to reorient images in a batch. The reorientation parameters can be given either as a 4x4 matrix or as parameters as defined for spm_matrix.m. The new image orientation will be computed by PRE-multiplying the original orientation matrix with the supplied matrix.'};
 reorient.prog = @spm_run_reorient;
 reorient.vout = @vout;