[FieldTrip] Problem with coordinate systems when creating head model

[Maria Hakonen]

Dear fieldtrip experts,

I would need to create a volume conduction model of the head using
standard_mri.m. standard_mri.m is in the spm coordinate system and my MEG
data in the neuromag system. To get all data in the same coordinate system,
I have converted standard_mri.m to neuromag using ft_volumerealign.
However, ft_volumesegment converts MRI back to spm.

Could someone please let me know how I can get the head model and MEG data
in the same coordinate system?
I really appreciate any help you can provide!

Here is what I have tried:

mri is in spm coordinate system:

mri =

          dim: [181 217 181]
      anatomy: [181x217x181 uint8]
    transform: [4x4 double]
          hdr: [1x1 struct]
         unit: 'mm'
     coordsys: 'spm'

Check fiducials for ft_volumerealign:

hs=ft_read_headshape('aml_sentences16b_raw_tsss.fif', 'unit','mm');

hs.fid.pos

ans =

  -66.1226    0.0000   -0.0000
   -0.0000   83.5082   -0.0000
   67.1784   -0.0000   -0.0000

hs.fid.label

ans =

    'LPA'
    'Nasion'
    'RPA'

cfg = [];
cfg.method= 'fiducial';
cfg.fiducial.nas    = [-0.0000 83.5082 -0.0000];
cfg.fiducial.lpa    = [-66.1226 0.0000 -0.0000];
cfg.fiducial.rpa    = [67.1784 -0.0000 -0.0000];
cfg.coordsys= 'neuromag';
cfg.headshape = hs;
mri_realigned = ft_volumerealign(cfg, mri);

mri_realigned seems to be in neuromag system as it should be.

mri_realigned =

              dim: [181 217 181]
          anatomy: [181x217x181 uint8]
        transform: [4x4 double]
              hdr: [1x1 struct]
             unit: 'mm'
         coordsys: 'neuromag'
           inside: [181x217x181 logical]
    transformorig: [4x4 double]
              cfg: [1x1 struct]

However, ft_volumesegment converts it back to spm system:
cfg           = [];
cfg.output    = 'brain';
cfg.coordsys  = 'neuromag';
segmentedmri  = ft_volumesegment(cfg, mri_realigned);

Warning: The option cfg.coordsys is deprecated, support is no longer
guaranteed

> In ft_checkconfig (line 168)
  In ft_volumesegment (line 170)
the input is volume data with dimensions [181 217 181]
Converting the coordinate system from neuromag to spm


I also tried to convert MEG data to spm system as follows:

hdr = ft_read_header('aml_sentences16b_raw_tsss.fif', 'unit','mm');

cfg = [];
cfg.method= 'fiducial';
cfg.target.pos(1,:)    = [1 0 0];
cfg.target.pos(1,:)    = [0 83 0];
cfg.target.pos(1,:)    = [0 -117 0];
cfg.target.lab    = {'NAS', 'LPA', 'RPA'};
cfg.grad = hdr.grad;
mri_realigned = ft_sensorrealign(cfg);

… but got:

Warning: FT_SENSORREALIGN is deprecated, please use FT_ELECTRODEREALIGN
instead.
> In ft_sensorrealign (line 118)
using gradiometers specified in the configuration
Reference to non-existent field 'label'.

Error in ft_datatype_sens (line 148)
nchan = length(sens.label);

Error in ft_sensorrealign (line 247)
    tmp(i) = ft_datatype_sens(template(i));            % ensure up-to-date
sensor description

template(i) seems to be as follows:

ans =

    pos: [0 -117 0]
    lab: {'NAS'  'LPA'  'RPA'}

I think that ft_electroderealign only works with EEG data since it gives:

mri_realigned = ft_electroderealign(cfg);
Warning: The field cfg.headshape is forbidden, it will be removed from your
configuration

> In ft_checkconfig (line 215)
  In ft_electroderealign (line 212)
using gradiometers specified in the configuration
Reference to non-existent field 'elecpos'.

Error in ft_electroderealign (line 254)
assert(isequaln(elec_original.elecpos, elec_original.chanpos), 'this
function requires same electrode and channel
positions.');

Best,
Maria
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