[FieldTrip] Interpolate, normalise and sourcegrandaverage with MNE

Sara Aurtenetxe s.aurtenetxe at bcbl.eu
Tue Sep 29 17:27:57 CEST 2015

Dear all, 

I am working on the source analysis of ERF data from ElektaNeuromag system, with individual T1s, using minimum-norm estimate as described in the following tutorial:
I am exactly following the suggested steps, and so got the source estimation for each of my subjects (bellow the output for one subject), which i can nicely plot with the ft_plot_mesh function:

sourceest = 

      time: [1x1401 double]
    inside: [8196x1 logical]
       pos: [8196x3 double]
    method: 'average'
       avg: [1x1 struct]
       cfg: [1x1 struct] 

Now, prior to a ft_sourcegrandaverage and ft_sourcestatistics, 
I am trying to normalise (ft_volumenormalise) and interpolate (ft_sourceinterpolate) the functional and anatomical data. 

However, I am struggling in this two last steps. 
Since I did not find a clear pipeline/tutorial about the exact approach (am I missing something?) 
and after trying several options (bellow I copy the code I am using), it is not clear to me:

- which is the exact input data for each of these last two functions, and
- in which order they should be called.

Now, I would highly appreciate if anyone could give me any cue about which the correct approach is.

Thank you in advance, 

All the best,



% Inverse solution
cfg        = [];
cfg.method = 'mne';
cfg.grid   = leadfield;
cfg.vol    = vol;
cfg.mne.prewhiten = 'yes';
cfg.mne.lambda    = 3;
cfg.mne.scalesourcecov = 'yes';
cfg.senstype = 'MEG';
sourceest  = ft_sourceanalysis(cfg,erf);

% read T1 volume - coords in scanner space
mri = ft_read_mri('s01.nii');
mri.coordsys = 'neuromag';

% read headshape - Neuromag coords
hsf = 's01.fif';
[headshape] = ft_read_headshape(hsf);

% align T1 with head posiiton in MEG
cfg = [];
cfg.method = 'headshape';
cfg.parameter      = 'anatomy';
cfg.headshape.headshape = headshape;
cfg.headshape.interactive = 'no';

mri_real = ft_volumerealign(cfg,mri);

% normalize the realinged individual MRI to SPM template
cfg = [];
cfg.spmversion  = 'spm8';
 % cfg.template='T1.nii'; % when enabling this field, an incoming error message indicates that the template is not in the spm coordinate system. 
                          % However, is the one used by default in this function (as mentioned in the reference) so it is confusing to me

norm_mri = ft_volumenormalise(cfg,mri_real);

% interpolate Source with MEG-aligned T1
cfg            = [];
cfg.parameter = 'all';
cfg.downsample = 2;

source_int  = ft_sourceinterpolate(cfg, sourceest,norm_mri);


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