avw2brainstorm

 avw2brainstorm - Convert Analyze struct into BrainStorm file
 
 avw2brainstorm(avw,[segment],[scalp],[PCS],[comment])
 
 This function saves a brainstorm file with a name that combines
 avw.fileprefix with _subjectimage.mat - for example, if
 avw.fileprefix is set to 'subject01', this function will
 output a brainstorm MRI file, in the current working
 directory, called 'subject01_subjectimage.mat'
 
 avw       - Analyze data loaded by avw_img_read.
 segment   - a sparse 3D matrix the same size as avw.img, with
             zeros (not brain) and other integer flags to indicate
             different tissue types (as yet unknown values!)
 scalp     - an Nx3 series of vertex points on the scalp, with
             coordinates in the Patient Coordinate System (PCS).
 PCS       - a struct with the fields described below
 comment   - a char array describing the image
 
 PCS contains the following fields:
 
 PCS.R % [3x3 double] rotations from PCS to MRI
 PCS.t % [3x1 double] translations from PCS to MRI
 PCS.Comment % a char array describing the PCS 
             % orientation (always 'Neuromag 122' here)
 PCS.PCSFiducial  % [3x4 double] of electrode fiducials
 PCS.CubeFiducial % [3x4 double] of MRI fiducials
 PCS.FiducialName = {'Nasion'  'LeftEar'  'RightEar'  'Origin'};
 
 see also AVW_VIEW & ELEC_COREGISTER to obtain fiducials and
 calculate T, where PCS.R = T(1:3;1:3) and PCS.t = T(4,1:3).

 See http://neuroimage.usc.edu/ for more information about
 brainstorm, including a download PDF of the file formats.

0001 function avw2brainstorm(avw,Segment,Scalp,PCS,Comment)
0002 
0003 % avw2brainstorm - Convert Analyze struct into BrainStorm file
0004 %
0005 % avw2brainstorm(avw,[segment],[scalp],[PCS],[comment])
0006 %
0007 % This function saves a brainstorm file with a name that combines
0008 % avw.fileprefix with _subjectimage.mat - for example, if
0009 % avw.fileprefix is set to 'subject01', this function will
0010 % output a brainstorm MRI file, in the current working
0011 % directory, called 'subject01_subjectimage.mat'
0012 %
0013 % avw       - Analyze data loaded by avw_img_read.
0014 % segment   - a sparse 3D matrix the same size as avw.img, with
0015 %             zeros (not brain) and other integer flags to indicate
0016 %             different tissue types (as yet unknown values!)
0017 % scalp     - an Nx3 series of vertex points on the scalp, with
0018 %             coordinates in the Patient Coordinate System (PCS).
0019 % PCS       - a struct with the fields described below
0020 % comment   - a char array describing the image
0021 %
0022 % PCS contains the following fields:
0023 %
0024 % PCS.R % [3x3 double] rotations from PCS to MRI
0025 % PCS.t % [3x1 double] translations from PCS to MRI
0026 % PCS.Comment % a char array describing the PCS
0027 %             % orientation (always 'Neuromag 122' here)
0028 % PCS.PCSFiducial  % [3x4 double] of electrode fiducials
0029 % PCS.CubeFiducial % [3x4 double] of MRI fiducials
0030 % PCS.FiducialName = {'Nasion'  'LeftEar'  'RightEar'  'Origin'};
0031 %
0032 % see also AVW_VIEW & ELEC_COREGISTER to obtain fiducials and
0033 % calculate T, where PCS.R = T(1:3;1:3) and PCS.t = T(4,1:3).
0034 %
0035 % See http://neuroimage.usc.edu/ for more information about
0036 % brainstorm, including a download PDF of the file formats.
0037 %
0038 
0039 % $Revision: 1.1 $ $Date: 2004/11/12 01:30:25 $
0040 
0041 % Licence:  GNU GPL, no express or implied warranties
0042 % Author:   10/2002, Darren.Weber@flinders.edu.au
0043 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0044 
0045 fprintf('AVW2BRAINSTORM...\n'); tic
0046 
0047 if ~exist('avw','var'),
0048     msg = sprintf('...no input avw - see help avw2brainstorm\n');
0049     error(msg);
0050 end
0051 
0052 fprintf('...converting avw to brainstorm variables\n');
0053 
0054 Cube = uint8(avw.img);
0055 
0056 Voxsize = double(avw.hdr.dime.pixdim(2:4));
0057 
0058 if ~exist('Comment','var'),
0059     if isfield(avw,'fileprefix'),
0060         Comment = avw.fileprefix;
0061     else
0062         Comment = '';
0063     end
0064 end
0065 
0066 if ~exist('Segment','var'), Segment = []; end
0067 
0068 if ~exist('Scalp','var'), Scalp = []; end
0069 
0070 if ~exist('PCS','var'),
0071     PCS.R = eye(3);     % [3x3 double] rotations
0072     PCS.t = zeros(3,1); % [3x1 double] translations
0073     PCS.Comment = 'Neuromag 122';
0074     PCS.PCSFiducial  = []; % [3x4 double]
0075     PCS.CubeFiducial = []; % [3x4 double]
0076     PCS.FiducialName = {'Nasion'  'LeftEar'  'RightEar'  'Origin'};
0077 else
0078     PCS.Comment = 'Neuromag 122';
0079 end
0080 
0081 savename = sprintf('%s_subjectimage.mat',avw.fileprefix);
0082 
0083 fprintf('...saving brainstorm variables to %s\n', savename);
0084 
0085 save(savename,'Cube','Voxsize','Comment','Segment','Scalp','PCS');
0086 
0087 t=toc; fprintf('...done (%5.2f sec).\n\n',t);
0088 
0089 return