feConnectomeSetDwi

 Set all the fields necessary to store the DWI measurements.

 This can be used for the dwi measurements use to build the model as well
 as for those used as a second repeat.

 Inputs:
   fe          - an fe structure
   dwiFileName - the full path to a dwi nifti file
   isrepeat    - wether the file being set up is the origianl data used to
                 build LiFE or a repeated measurements used to compute 
                 statistcs of the quality of fit.        
 Outputs:
   fe - fe structure with data added in the appropriate fields.
  
 fe = feConnectomeSetDwi(fe,dwiFileName);   % Set the original data
 fe = feConnectomeSetDwi(fe,dwiFileName,1); % Set the repeated measure
                                            % data

 Copyright (2013-2014), Franco Pestilli, Stanford University, pestillifranco@gmail.com.

0001 function fe = feConnectomeSetDwi(fe,dwiFileName,isrepeat)
0002 % Set all the fields necessary to store the DWI measurements.
0003 %
0004 % This can be used for the dwi measurements use to build the model as well
0005 % as for those used as a second repeat.
0006 %
0007 % Inputs:
0008 %   fe          - an fe structure
0009 %   dwiFileName - the full path to a dwi nifti file
0010 %   isrepeat    - wether the file being set up is the origianl data used to
0011 %                 build LiFE or a repeated measurements used to compute
0012 %                 statistcs of the quality of fit.
0013 % Outputs:
0014 %   fe - fe structure with data added in the appropriate fields.
0015 %
0016 % fe = feConnectomeSetDwi(fe,dwiFileName);   % Set the original data
0017 % fe = feConnectomeSetDwi(fe,dwiFileName,1); % Set the repeated measure
0018 %                                            % data
0019 %
0020 % Copyright (2013-2014), Franco Pestilli, Stanford University, pestillifranco@gmail.com.
0021 
0022 % Check inputs
0023 if notDefined('isrepeat'), isrepeat=0;end
0024 
0025 % Build a tag for the calls to feSet.
0026 if isrepeat, tag = sprintf('repeat');
0027 else         tag = sprintf('');
0028 end
0029 
0030 % Set the ile name in the structure
0031 fe  = feSet(fe, sprintf('dwi%sfile',tag),dwiFileName);
0032 
0033 % load the dwi data
0034 dwi = feGet(fe, sprintf('dwi%s',tag));
0035 
0036 % Store the bvecs, bvals and the indices for the new file.
0037 fe  = feSet(fe, sprintf('diffusion bvecs %s',tag), ...
0038             dwiGet(dwi, 'diffusion bvecs'));
0039 fe  = feSet(fe, sprintf('diffusion bvals %s',tag), ...
0040             dwiGet(dwi, 'diffusion bvals'));
0041 fe  = feSet(fe, sprintf('bvecs indices %s',tag),   ...
0042             dwiGet(dwi, 'diffusionimagenums'));
0043 
0044 % Extract the dwi signal at the coordinates of the connectome
0045 fe  = feSet(fe, sprintf('diffusion signal image %s',tag), ...
0046             dwiGet(dwi, 'diffusion signal image',feGet(fe,'roi coords')) );
0047           
0048 % Extract the non-diffusion direction signal at the coordinates of the
0049 % conenctome
0050 fe  = feSet(fe, sprintf('S0 image %s',tag), ...
0051             dwiGet(dwi, 'S0 image',feGet(fe,'roi coords')));
0052 
0053 if length(isrepeat)>1, keyboard;end
0054           
0055 % Here I set the dimensions of the dwi file so that I have that
0056 % available everytime when creating a map of parameters.
0057 fe = feSet(fe,sprintf('img size %s',tag),dwiGet(dwi,'size'));
0058 
0059 end