[FieldTrip] Fw: ft_prepare_layout rotate axis does not work in the new Fieldtrip release

[Elisa Tatti]

Dear Fieldtrip community,
I am writing to ask for help with creating the channel layout using the function ft_prepare_layout. I have two questions:


  1.  In the past, I successfully used the option cfg.rotate to rotate the axis of 90 degrees due to the differences in orientation between eeglab and fieldtrip. In the latest Fieldtrip (20230118) version, the option cfg.rotate does not work anymore. It does not give any error and it creates the layout but it does not rotate the axis. I ran the function with cfg.rotate both as default [] (which should automatically rotate the axis) and with different rotations (90,180). I checked the output and it seems it is not rotating the axis at all.
I compared it with a previous version (20200607) (where it works perfectly) and noticed that parts of the code have been changed. Specifically, in ft_prepare_layout in Fieldtrip 20200607 the section that rotates the axis using ft_warp_apply (lines 1291-1307, see below) in the subfunction sens2lay has been changed in Fieldtrip 20230118. I can see the function ft_warp_apply for the subfunction opto2lay but it is not there for sens2lay anymore. I am unsure if that is actually what it was meant to be done and it is okay like this but may this be the reason why it does not rotate anymore?

Old Fieldtrip function:

% apply rotation, but only if viewpoint is not used specifically
if isempty(viewpoint)
  if isempty(rotatez)
    switch ft_senstype(sens)
      case {'ctf151', 'ctf275', 'bti148', 'bti248', 'ctf151_planar', 'ctf275_planar', 'bti148_planar', 'bti248_planar', 'yokogawa160', 'yokogawa160_planar', 'yokogawa64', 'yokogawa64_planar', 'yokogawa440', 'yokogawa440_planar', 'magnetometer', 'meg'}
        rotatez = 90;
      case {'neuromag122', 'neuromag306'}
        rotatez = 0;
      case 'electrode'
        rotatez = 90;
      otherwise
        rotatez = 0;
    end
  end
  sens.chanpos = ft_warp_apply(rotate([0 0 rotatez]), sens.chanpos, 'homogenous');
end

Fieldtrip 20230118

% apply rotation, but only if viewpoint is not used specifically
if isempty(viewpoint) && isempty(rotatez)
  if isfield(sens, 'coordsys')
    % the x-axis to the right of the screen and the y-axis is to the top of the screen
    % the nose is usually plotted toward the top of the screen
    sens = ft_convert_coordsys(sens, 'ras', 0);
  elseif isfield(sens, 'type') && startsWith(sens.type, 'ctf')
    sens.coordsys = 'ctf';
    sens = ft_convert_coordsys(sens, 'ras', 0);
  elseif isfield(sens, 'type') && startsWith(sens.type, 'bti')
    sens.coordsys = 'bti';
    sens = ft_convert_coordsys(sens, 'ras', 0);
  elseif isfield(sens, 'type') && startsWith(sens.type, '4d')
    sens.coordsys = '4d';
    sens = ft_convert_coordsys(sens, 'ras', 0);
  elseif isfield(sens, 'type') && startsWith(sens.type, 'yokogawa')
    sens.coordsys = 'yokogawa';
    sens = ft_convert_coordsys(sens, 'ras', 0);
  elseif isfield(sens, 'type') && startsWith(sens.type, 'neuromag')
    sens.coordsys = 'neuromag';
    sens = ft_convert_coordsys(sens, 'ras', 0);
  elseif isfield(sens, 'type') && startsWith(sens.type, 'itab')
    sens.coordsys = 'itab';
    sens = ft_convert_coordsys(sens, 'ras', 0);
  else
    ft_warning('use cfg.rotate to specify the correct rotation of the sensors');
  end
end

If anyone has information about it, please share it with the community. Thank you!

  1.  Using the old Fieldtrip version, I created the layout using ft_prepare_layout and 90 degrees rotation to have the frontal channels oriented toward the nose. However, when I plot the channels with the function ft_plot_layout, they look too centered in the middle (see the attached image with a comparison between the EEGLAB channel layout and the output of ft_prepare_layout. What can I do to fix them?

Thank you in advance for your help!

Best.

Elisa





Elisa Tatti, Ph.D.


Research Associate

Research Foundation of the City University of New York

CUNY, School of Medicine

160 Convent ave

New York City, NY, 10031


Adjunct Assistant Professor

College of Staten Island,

2800 Victory Blvd, Staten Island, NY 10314


Tel. +1 3472043952

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