[FieldTrip] Pipeline for sourceanalysis with individualize grid.

Thu Mar 10 08:55:54 CET 2016

Hi Olga,

The ‘template grid’ refers to a so-called source model, i.e. the set of positions that you use to model your sources.
The headmodel refers to the volume conduction model of the head.

The inverse warping is intended to facilitate group comparisons after the source reconstruction.

For the source reconstruction you can use these ‘inverse warped template grids’, but it is advisable to always use a volume conduction model based on the participant’s anatomy, as Simon already suggested in his reply.

Best wishes,
Jan-Mathijs

On 09 Mar 2016, at 17:18, Olga Sysoeva <olga.v.sysoeva at gmail.com<mailto:olga.v.sysoeva at gmail.com>> wrote:

Dear Simon,

Thank you very much for the answer, but I think that this code should "create the subject specific grid, using the template grid" as specified in tutorial here http://www.fieldtriptoolbox.org/tutorial/sourcemodel.
"

% create the subject specific grid, using the template grid that has just been created
cfg                = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.warpmni   = 'yes';
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.template  = template_grid;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.nonlinear = 'yes'; % use non-linear normalization
cfg.mri            = mri;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.unit      ='mm';
grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>               = ft_prepare_sourcemodel(cfg);

I believe it "align/project" the template grid with individual mri using non-linear transformation.

Correct me if I'm wrong.
I'll be more than happy to get more comments on this.

Best Regards,
Olga.

On Wed, Mar 9, 2016 at 2:43 PM, Simon Homolle <s.homolle at donders.ru.nl<mailto:s.homolle at donders.ru.nl>> wrote:
Dear Olga,

Should I use template or subject-specific headmodel with “projected to template grid individualized grid”?

I would use the individual head model based on the MRI as it provides more information for your source analysis. This should provide more accurate results.

Actually I tried both ways for one subject and did not notice any difference in the results.

It seems to that this is due to this line of code, but I’m not quite sure about that:

cfg = [];

cfg.grid.warpmni = 'yes';

cfg.grid.template = template_grid;

cfg.grid.nonlinear = 'yes'; % use non-linear normalization

cfg.mri = mri_cm{Subj_i};

grid_ind{Subj_i} = ft_prepare_sourcemodel(cfg);

I think with this configuration the source model that is prepared is only based on the cfg.grid.template, and completely ignores the MRI (which you are interested in). This might explain why you see no difference.

Bests,

Simon Homölle
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Phone: +31-(0)24-36-65059

On 09 Mar 2016, at 11:57, Olga Sysoeva <olga.v.sysoeva at gmail.com<mailto:olga.v.sysoeva at gmail.com>> wrote:

Pipeline for sourceanalysis with individualize grip

Dear field trippers,

I have a question related to pipeline for sourceanalysis with individualize grid.

Should I use template or subject-specific headmodel with “projected to template grid individualized grid”? Below is my pipeline with details of what I mean. Actually I tried both ways for one subject and did not notice any difference in the results. Does it mean that I do not need to constract headmodel for each subject? That's indeed save a lot of time, but I'd like to get your green light on this.

Best Regards,

Olga.

% 1. load template grid, e.g.

load('/net/server/mnt/programs/olgas/fieldtrip-20160119/template/sourcemodel/standard_sourcemodel3d10mm.mat');

template_grid = sourcemodel;

%2. Make the individual subjects' grid

%a) Load individual subject mri, e.g.

[mri{Subj_i}] = ft_read_mri(path_MRI{Subj_i});

mri_cm{Subj_i} = ft_convert_units(mri{Subj_i}, 'cm');

%b) construct individual grid by projecting to template grid

cfg = [];

cfg.grid.warpmni = 'yes';

cfg.grid.template = template_grid;

cfg.grid.nonlinear = 'yes'; % use non-linear normalization

cfg.mri = mri_cm{Subj_i};

grid_ind{Subj_i} = ft_prepare_sourcemodel(cfg);

% 3. Make source reconstruction, using individualized grid and template? or individual headmodel

%a) load template volume load('/net/server/data/programs/olgas/fieldtrip-20160119/template/headmodel/standard_singleshell.mat');

template_vol = vol;

cfg = [];

cfg.grid = grid_ind{Subj_i};

cfg.vol = vol_K0012_cm; % individual or template vol???

cfg.channel = {'MEG'};

cfg.grad = freq_cmb{Subj_i}.grad;

sourcemodel_lf_K0012 = ft_prepare_leadfield(cfg, freq_cmb{Subj_i});

cfg = [];

cfg.frequency = freq_cmb{Subj_i}.freq;

cfg.grad = freq_cmb{Subj_i}.grad;

cfg.method = 'dics';

cfg.keeptrials = 'yes';

cfg.grid = sourcemodel_lf{Subj_i}; % sourcemodel after leadfield with individual or template headmodel?

cfg.vol = vol_K0012_cm; % individual or template vol???

cfg.keeptrials = 'yes';

cfg.dics.lambda = '5%';

cfg.dics.keepfilter = 'yes';

cfg.dics.fixedori = 'yes';

cfg.dics.realfilter = 'yes';

source_K0012 = ft_sourceanalysis(cfg, freq_cmb{Subj_i});

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