[FieldTrip] Pipeline for sourceanalysis with individualize grid.

[Olga Sysoeva]

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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