<div dir="ltr">
<div class="" lang="x-western">
  

    
  
  
    <div class="" style="font-family:-moz-fixed;font-size:14px" lang="x-western">Dear Fieldtrippers!
      <br>
      As newbie I have another question, now concerning the warping from
      MNI to individual subjects.
      <br>
      Using the below code (the first part almost entirely from <a class="" href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space</a>),
      I get first the template and then apply the grid to the individual
      subjects.
      <br>
      However, in later on analysis step it turned out that while the
      subjects where nicely similar positioned, the template position is
      entirely different, as it is was even axes were exchanged...
      <br>
      Does anybody know what could be the reason and how to change it?
      <br>
      Thanks for any suggestions!
      <br>
      Best, Meike
      <br>
      <br>
      <br>
      % NOTE: the path to the template file is user-specific
      <br>
      template =
ft_read_mri('fieldtrip/fieldtrip-20140316/external/spm8/templates/T1.nii');<br>
      template.coordsys = 'spm'; % so that FieldTrip knows how to
      interpret the coordinate system
      <br>
      <br>
      % segment the template brain and construct a volume conduction
      model (i.e. head model): this is needed
      <br>
      % for the inside/outside detection of voxels.
      <br>
      cfg          = [];
      <br>
      template_seg = ft_volumesegment(cfg, template);
      <br>
      <br>
      cfg          = [];
      <br>
      cfg.method   = 'singleshell';
      <br>
      template_vol = ft_prepare_headmodel(cfg, template_seg);
      <br>
      template_vol = ft_convert_units(template_vol, 'cm'); % Convert the
      vol to cm, since the grid will also be expressed in cm
      <br>
      <br>
      % construct the dipole grid in the template brain coordinates
      <br>
      % the source units are in cm
      <br>
      % the negative inwardshift means an outward shift of the brain
      surface for inside/outside detection
      <br>
      cfg = [];
      <br>
      cfg.grid.xgrid  = -20:1:20;
      <br>
      cfg.grid.ygrid  = -20:1:20;
      <br>
      cfg.grid.zgrid  = -20:1:20;
      <br>
      cfg.grid.unit   = 'cm';
      <br>
      cfg.grid.tight  = 'yes';
      <br>
      cfg.inwardshift = -1.5;
      <br>
      cfg.vol        = template_vol;
      <br>
      template_grid  = ft_prepare_sourcemodel(cfg);
      <br>
save('../analysis/MEG/source_analysis/MNI','template_grid','template_vol','template_seg','template')
      <br>
      % make a figure with the template head model and dipole grid
      <br>
      figure
      <br>
      hold on
      <br>
      ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
      'none');alpha 0.5; camlight;
      <br>
      ft_plot_mesh(template_grid.pos(template_grid.inside,:));
      <br>
      else
load('../analysis/MEG/source_analysis/MNI','template_grid','template_vol','template_seg','template')<br>
      <br>
      <br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      <br>
           SUBJECTS={    'VP02'    'VP03'    'VP04'    'VP05'    'VP06'
      'VP07'    'VP08'    'VP09'    'VP11'    'VP12'    'VP13' 'VP14'   
      'VP15'    'VP16'    'VP17'    'VP18'}
      <br>
      <br>
      for SUBJI=SUBJECTS
      <br>
          SUBJ=SUBJI{1};
      <br>
      % read the single subject anatomical MRI
      <br>
      load(['..<i class=""><span class="">/</span>analysis/MEG/source_analysis<span class="">/</span></i>',SUBJ,'/mri']);  %Has been
      processed to CFT coordinates before
      <br>
      load(['..<i class=""><span class="">/</span>analysis/MEG/source_analysis<span class="">/</span></i>',SUBJ,'/segmentedmri']);
      <br>
      <br>
      <br>
      cfg = [];
      <br>
      cfg.method = 'singleshell';
      <br>
      vol = ft_prepare_headmodel(cfg, segmentedmri);
      <br>
      <br>
      % create the subject specific grid, using the template grid that
      has just been created
      <br>
      cfg = [];
      <br>
      cfg.grid.warpmni   = 'yes';
      <br>
      cfg.grid.template  = template_grid;
      <br>
      cfg.grid.nonlinear = 'yes'; % use non-linear normalization
      <br>
      cfg.mri            = mri_ra;
      <br>
      grid               = ft_prepare_sourcemodel(cfg);
      <br>
      <br>
      % make a figure of the single subject headmodel, and grid
      positions
      <br>
      figure;
      <br>
      ft_plot_vol(vol, 'edgecolor', 'none'); alpha 0.4; %camlight
      <br>
      ft_plot_mesh(grid.pos(grid.inside,:));
      <br>
      <br>
      save(['..<i class=""><span class="">/</span>analysis/MEG/source_analysis<span class="">/</span></i>',SUBJ,'/MNIgrid'],'grid','vol')
      <br>
      end
      <br>
      <br>
    </div>
  


</div>

</div>