Spm versioning

ExtractionScripts/BuildROI/BuildSphere_mc_template.m

@@ -42,7 +42,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'ExtractionScripts','BuildROI'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 

ExtractionScripts/BuildROI/Img2Mat_mc_template.m

@@ -45,7 +45,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'ExtractionScripts','BuildROI'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 Img2Mat_central   

ExtractionScripts/ExtractROI/ExtractROI_mc_template.m

@@ -42,7 +42,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'ExtractionScripts','ExtractROI'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 ExtractROI_central

FirstLevel/FirstLevel_mc_template.m

@@ -397,7 +397,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'FirstLevel'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 Processing = [0 1];

FirstLevel/Preprocess_mc_template.m

@@ -211,7 +211,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'FirstLevel'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 

MotionRegressors/MVMT_collapse_mc_template.m

@@ -96,7 +96,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'MotionRegressors'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 

MotionSummary/MotionSummary_mc_template.m

@@ -138,7 +138,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'MotionSummary'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 

PhysioSummary/PhysioSummary_mc_template.m

@@ -176,7 +176,7 @@
 
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'PhysioSummary'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 

QualityChecks/CheckReg/CheckReg_mc_template.m

@@ -107,7 +107,7 @@
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'QualityChecks','CheckReg'))
 addpath(fullfile(mcRoot,'QualityChecks','CheckWarp'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
 

QualityChecks/CheckWarp/CheckWarp_mc_template.m

@@ -109,7 +109,7 @@
 addpath(fullfile(mcRoot,'matlabScripts'))
 addpath(fullfile(mcRoot,'QualityChecks','CheckReg'))
 addpath(fullfile(mcRoot,'QualityChecks','CheckWarp'))
-addpath(fullfile(mcRoot,'spm8'))
+addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))
 
 
    CheckWarp_central

SPM/SPM5/@file_array/Contents.m

@@ -0,0 +1,51 @@
+%
+% File Array Object
+%
+%   file_array   - create a file_array
+%   horzcat      - horizontal concatenation
+%   vertcat      - vertical concatenation
+%   size         - size of array
+%   length       - length of longest dimension
+%   subsref      - subscripted reference
+%   end          - last index in an indexing expression
+%   resize       - resize (but only of simple file_array structures)
+%
+%   other operations are unlikely to work.
+%
+% Example usage.
+%
+% % Create a file array object by mapping test_le.img
+% % to a 256x256x100 array, of datatype float32, stored
+% % in a little-endian way starting at byte 0.
+% fa0 = file_array('test_le.img',[256 256 100], 'FLOAT32-LE',0)
+%
+% % Creating an object from test_be.img, but skipping
+% % the first plane of data.  Data stored as big-endian
+% fa1 = file_array('test_be.img',[256 256 99], 'FLOAT32-BE',4*256*256)
+%
+% % Reshape procedure
+% fa2 = reshape(fa1,[128 2 256 99])
+%
+% % Concatenation
+% fa3 = [[fa0 fa0]; [fa0 fa0]]
+% fa4 = cat(3,fa0,fa1)
+%
+% % Note that reshape will not work on the above
+% % concatenated objects
+%
+% % Accessing values from the objects
+% img    = fa1(:,:,40);
+% pixval = fa4(50,50,:);
+% small  = fa1(1:2:end,1:2:end,40);
+%
+% % Determining dimensions
+% size(fa4)
+% size(fa2)
+% length(fa0)
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: Contents.m 1601 2008-05-12 14:11:02Z guillaume $
+
+

SPM/SPM5/@file_array/cat.m

@@ -0,0 +1,40 @@
+function o = cat(dr,varargin)
+% Concatenate file_array objects.  The result is a non-simple object
+% that can no longer be reshaped.
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: cat.m 253 2005-10-13 15:31:34Z guillaume $
+
+
+if dr>32 || dr<0, error('Unknown command option.'); end;
+dr   = max(round(dr),1);
+d    = ones(nargin-1,16);
+tmp  = {};
+dpos = 0;
+for i=1:nargin-1,
+    vi = varargin{i};
+    if strcmp(class(vi),'file_array')
+        sz                = size(vi);
+        d(i,1:length(sz)) = sz;
+        svi               = struct(vi);
+        svi               = svi(:);
+        for j=1:length(svi(:)),
+            if length(svi(j).pos)<dr
+                svi(j).pos((length(svi(j).pos)+1):dr) = 1;
+            end
+            svi(j).pos(dr)= svi(j).pos(dr) + dpos;
+        end;
+        dpos              = dpos + d(i,dr);
+        tmp{i}            = svi;
+    else
+        error(['Conversion to file_array from ' class(vi) ' is not possible.']);
+    end;
+end;
+if any(diff(d(:,[1:(dr-1) (dr+1):end]),1,1))
+    error('All matrices on a row in the bracketed expression must have the same number of rows.');
+else
+    o = vertcat(tmp{:});
+    o = class(o,'file_array');
+end;

SPM/SPM5/@file_array/ctranspose.m

@@ -0,0 +1,9 @@
+function varargout = ctranspose(varargin)
+% Transposing not allowed
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: ctranspose.m 253 2005-10-13 15:31:34Z guillaume $
+
+error('file_array objects can not be transposed.');

SPM/SPM5/@file_array/disp.m

@@ -0,0 +1,34 @@
+function disp(obj)
+% Display a file_array object
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: disp.m 253 2005-10-13 15:31:34Z guillaume $
+
+
+if numel(struct(obj))>1,
+    fprintf('       %s object: ', class(obj));
+    sz = size(obj);
+    if length(sz)>4,
+        fprintf('%d-D\n',length(sz));
+    else
+        for i=1:(length(sz)-1),
+            fprintf('%d-by-',sz(i));
+        end;
+        fprintf('%d\n',sz(end));
+    end;
+else
+    display(mystruct(obj))
+end;
+return;
+%=======================================================================
+
+%=======================================================================
+function t = mystruct(obj)
+fn = fieldnames(obj);
+for i=1:length(fn)
+    t.(fn{i}) = subsref(obj,struct('type','.','subs',fn{i}));
+end;
+return;
+%=======================================================================

SPM/SPM5/@file_array/display.m

@@ -0,0 +1,14 @@
+function display(obj)
+% Display a file_array object
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: display.m 253 2005-10-13 15:31:34Z guillaume $
+
+
+disp(' ');
+disp([inputname(1),' = '])
+disp(' ');
+disp(obj)
+disp(' ')

SPM/SPM5/@file_array/double.m

@@ -0,0 +1,12 @@
+function out = double(fa)
+% Convert to double precision
+% FORMAT double(fa)
+% fa - a file_array
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: double.m 253 2005-10-13 15:31:34Z guillaume $
+
+out = double(numeric(fa));
+

SPM/SPM5/@file_array/end.m

@@ -0,0 +1,17 @@
+function en = end(a,k,n)
+% Overloaded end function for file_array objects.
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: end.m 253 2005-10-13 15:31:34Z guillaume $
+
+dim = size(a);
+if k>length(dim)
+    en = 1;
+else
+    if n<length(dim),
+	dim = [dim(1:(n-1)) prod(dim(n:end))];
+    end;
+    en = dim(k);
+end;

SPM/SPM5/@file_array/fieldnames.m

@@ -0,0 +1,16 @@
+function t = fieldnames(obj)
+% Fieldnames of a file-array object
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: fieldnames.m 253 2005-10-13 15:31:34Z guillaume $
+
+t = {...
+    'fname'
+    'dim'
+    'dtype'
+    'offset'
+    'scl_slope'
+    'scl_inter'
+};

SPM/SPM5/@file_array/file_array.m

@@ -0,0 +1,39 @@
+function a = file_array(varargin)
+% Function for creating file_array objects.
+% FORMAT a = file_array(fname,dim,dtype,offset,scl_slope,scl_inter)
+% a         - file_array object
+% fname     - filename
+% dim       - dimensions (default = [0 0] )
+% dtype     - datatype   (default = 'uint8-le')
+% offset    - offset into file (default = 0)
+% scl_slope - scalefactor (default = 1)
+% scl_inter - DC offset, such that dat = raw*scale + inter (default = 0)
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: file_array.m 315 2005-11-28 16:48:59Z john $
+
+
+if nargin==1
+    if isstruct(varargin{1}),
+        a = class(varargin{1},'file_array');
+        return;
+    elseif isa(varargin{1},'file_array'),
+        a = varargin{1};
+        return;
+    end;
+end;
+a = struct('fname','','dim',[0 0],'dtype',2,...
+           'be',0,'offset',0,'pos',[],'scl_slope',[],'scl_inter',[]);
+%a = class(a,'file_array');
+
+if nargin>=1, a =     fname(a,varargin{1}); end;
+if nargin>=2, a =       dim(a,varargin{2}); end;
+if nargin>=3, a =     dtype(a,varargin{3}); end;
+if nargin>=4, a =    offset(a,varargin{4}); end;
+if nargin>=5, a = scl_slope(a,varargin{5}); end;
+if nargin>=6, a = scl_inter(a,varargin{6}); end;
+
+a.pos = ones(size(a.dim));
+a     = class(a,'file_array');

SPM/SPM5/@file_array/horzcat.m

@@ -0,0 +1,11 @@
+function o = horzcat(varargin)
+% Horizontal concatenation of file_array objects
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: horzcat.m 253 2005-10-13 15:31:34Z guillaume $
+
+o    = cat(2,varargin{:});
+return;
+

SPM/SPM5/@file_array/length.m

@@ -0,0 +1,11 @@
+function l = length(x)
+% Overloaded length function for file_array objects
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: length.m 253 2005-10-13 15:31:34Z guillaume $
+
+
+l = max(size(x));
+

SPM/SPM5/@file_array/loadobj.m

@@ -0,0 +1,14 @@
+function b = loadobj(a)
+% loadobj for file_array class
+% _______________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+%
+% $Id: loadobj.m 1746 2008-05-28 17:43:42Z guillaume $
+
+if isa(a,'file_array')
+    b = a;
+else
+    a = rmfield(a, 'permission');
+    b = file_array(a);
+end

SPM/SPM5/@file_array/ndims.m

@@ -0,0 +1,12 @@
+function out = ndims(fa)
+% Number of dimensions
+%_______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: ndims.m 253 2005-10-13 15:31:34Z guillaume $
+
+
+out = size(fa);
+out = length(out);
+

SPM/SPM5/@file_array/numel.m

@@ -0,0 +1,14 @@
+function t = numel(obj)
+% Number of simple file arrays involved.
+% _______________________________________________________________________
+% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
+
+%
+% $Id: numel.m 253 2005-10-13 15:31:34Z guillaume $
+
+
+% Should be this, but it causes problems when accessing
+% obj as a structure.
+%t = prod(size(obj));
+
+t  = numel(struct(obj));