[FieldTrip] Pipeline for sourceanalysis with individualize grid.

Simon Homolle s.homolle at donders.ru.nl
Wed Mar 9 12:43:58 CET 2016


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> 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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