[FieldTrip] LCMV returns no time series?

[Peter Goodin]

Hi Sarang,

Regarding your point on that I should have the time series in source.avg.mom, the function only returns an n x 1 matrix. I've checked the averaged data and it does contain the channel x time series in av.avg, so I'm not really sure what's going on. 

Peter  



_______________________
Dr Peter Goodin,

Brain and Psychological Sciences Research Centre (BPsyC)
Swinburne University,
Hawthorn, Vic, 3122
________________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Sarang S. Dalal [sarang at cfin.au.dk]
Sent: Thursday, 16 June 2016 12:10 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] LCMV returns no time series?

Hi Peter,


If you've used the 'lcmv' method for ft_sourceanalysis, you ought to have the time series already contained in source.avg.mom.


I've been working a lot lately on improving the LCMV functionality, but unfortunately haven't had a chance to document much yet. Especially if you are not contrasting different conditions, you might want to try these parameters:

cfg.lcmv.weightnorm   = 'nai';  % this is a new option :-)
cfg.lcmv.fixedori     = 'yes';

I also prefer to turn off reducerank, but YMMV:
cfg.lcmv.reducerank   = 'no';



Finally I've also contributed a viewer that will greatly help visualizing your virtual time series together with the MRI. You can find it in the latest distributions of FieldTrip under fieldtrip/contrib/nutmegtrip. You'll also need a full version of SPM8 in your path (the external in FieldTrip doesn't have all the necessary functions).


You​​ can use it like this:

cfg = [];

cfg.mripath = '/path/to/mri/nii'  % must be in nifti (nii) format

cfg.funparameter = 'avg.mom'

% cfg.atlas = ft_read_atlas('ROI_MNI_V4.nii'); % [optional] you can get atlas labels, if your MRI and grid points are based on the MNI grid
nmt_sourceplot_spm8(cfg,ft_convert_units(source,'mm'));

Cheers,
Sarang


________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of Peter Goodin <pgoodin at swin.edu.au>
Sent: Wednesday, June 15, 2016 3:32 PM
To: FieldTrip discussion list
Subject: [FieldTrip] LCMV returns no time series?


Hi FieldTrip list,

I'm using LCMV on averaged data (covariancewindow='all') but find the returned source estimates only have a single point. Is there a way to specify the analysis returns the time series for each grid point?

Thanks,

Peter