[FieldTrip] Issues with: Sourcegrandaverage & Spatial Common Filter

[Sara Aurtenetxe]

Hi Tzvetan, 

Sorry for taking that long to respond.
 
Thank you for your answers!

1. As far as I observed, it is sufficient to specify 
source.pos = template_grid.pos, for the grandaverage and stats. 

Then interpolate the source estimation with the template. 

2. Thanks!

All the best,

Sara





Sara Aurtenetxe

----- Original Message -----
From: "Tzvetan Popov" <tzvetan.popov at uni-konstanz.de>
To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
Sent: Saturday, October 10, 2015 3:29:54 PM
Subject: Re: [FieldTrip] Issues with: Sourcegrandaverage & Spatial Common	Filter

Sorry
second line should read 
source.pnt =template_grid.pnt

> Am 10.10.2015 um 14:53 schrieb Tzvetan Popov <tzvetan.popov at uni-konstanz.de>:
> 
> Hi Sara,
> 1. The error stems from the fact that all dipole locations and their positions are warped in individual anatomy. After each individual source reconstruction you have to specify 
> source.pos = template_grid.pos
> source.pnt = template_grid.pos
> After this you can use ft_sourcegrandaverage, ft_sourcestatistics etc.
> 
> 2.) Yes, ideally all appended.
> 
> good luck,
> Tzvetan
> 
> 
>> Dear all, 
>> 
>> I am working on the localization of oscillatory sources using beamforming 
>> (http://www.fieldtriptoolbox.org/tutorial/beamformer). 
>> The data are recorded with Elekta-Neuromag,
>> the source estimations are based on individual MNI-aligned grids
>> (http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space), 
>> and the FT version is fieldtrip-20150701.
>> 
>> And I have two main issues, which would be very appreciated if someone could help me with:
>> 
>> 1. When SOURCEGRANDAVERAGING, "ERROR: the input sources vary in the field inside". Below this message you can see the code I am using.
>> 
>> Should I make additional normalization prior to / in the creation of the individual grid? 
>> I found this link which is specific to Neuromag data but it says is outdated (?). 
>> http://www.fieldtriptoolbox.org/example/read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
>> 
>> Or should I interpolate the source estimation to the template, instead of to the individual-mri?
>> When doing so (without after normalizing it), everything works fine but my plots looks like attached (grandavg of 7 subjects). 
>> 
>> 2. When creating a SPATIAL COMMON FILTER for comparing the Post stimulus sources of two conditions (effects were baseline corrected within condition in sensor space), 
>> should the Allappended input data include the Post-stimulus and Pre-stimulus intervals of each condition (e.g. PrestimA + PrestimB + PoststimA + PoststimB)?
>> 
>> 
>> Any comment would be very helpful! 
>> 
>> Thank you in advance, 
>> 
>> All the best,
>> 
>> Sara 
>> 
>> %%
>> 
>>   %% Interpolation, normalization and grandaverage
>> 
>>   load source mri_real template
>> 
>>   source.pos=template_grid.pos; % right(?) 
>> 
>>   cfg              = [];
>>   cfg.downsample   = 2;
>>   cfg.parameter    = 'pow';
>>   sourceInt        = ft_sourceinterpolate(cfg, source, mri_real);  
>> 
>>   cfg = [];
>>   cfg.spmversion   = 'spm8';
>>   %cfg.template    = '~/fieldtrip/external/spm8/templates/T1.nii'; 
>>                              % When enabling this parameter i get this error: "the head coordinate system of the template does not seem to be correspond with the mni/spm convention".
>>                              % However should be one taken by default and unablinginn it works fine so it is confussing (?)
>>   sourceIntNorm    = ft_volumenormalise(cfg, sourceInt);
>> 
>>   %% grand average for 7 subjects
>> 
>>   cfg=[];
>>   cfg.parameter    = 'pow';
>>   [grandavg]       = ft_sourcegrandaverage(cfg, sourceIntNorm{:});
>> 
>>   %%
>> 
>> %%
>> <gravg_int_templ.jpg>_______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
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