sourceinterpolation coordinates.

[jan-mathijs schoffelen]

Hi Hanneke,

This looks like a difference in origin to me. Note that the MNI  
coordinate system has the cardinal axes pointing in the same  
directions as the neuromag headcoordinate system, but that the origin  
is different. The origin of the NM-headcoordinate system is on the  
interauricular line, the point where the y-axis hits it. This is  
approximately somewhere close or in the pons. The MNI origin is the  
AC, which is somewhere 'higher' in the volume. I suspect that the  
preparation of the grids did not work out without flaws.
Alternatively, which I think is the most likely explanation, is that  
you should use the MNI-template as an MRI for the interpolation,  
rather than a normalized single subject MRI. I don't know about the  
single subject MRIs, but at least the MNI-template is explicitly in  
MNI-space, whereas the normalized MRI could be in head-space. This  
could explain the shift.
Anyway, if the latter hunch is the explanation, then the  
sourceanalysis results might be trusted, if the first hunch was the  
one, the sourceanalysis results are most certainly wrong.

As a matter of fact the whole swapping around with coordinates should  
not be necessary if the basic fieldtrip-code is adjusted such that it  
can handle neuromag-based headcoordinate systems in an appropriate  
way. This relates to an earlier remark on the list, which rightfully  
states that the approach you (we) have been taken so far seems a bit  
tedious. Ideally, in other words, the middle man has to be taken out,  
which in this case is the intermediate transformation to a ctf-based  
coordinate system.

Hope this helps,

JM


Quoting Hanneke van Dijk <Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE>:

> Now there is an attachment too! sorry
>
> On Fri, Jul 10, 2009 at 4:08 PM, Hanneke Van Dijk <
> Hanneke.vanDijk at med.uni-duesseldorf.de> wrote:
>
>> Dear all,
>>
>> I have entered the next step: sourceanalysis. But I have encountered
>> another problem, I think in sourceinterpolation or maybe volumenormalise.
>>
>> After running the script as I have described before (to make the headmodel
>> and the grid) I do the following;
>>
>> load f %load frequency data
>> cfg                = [];
>> cfg.grid           = grid;
>> cfg.frequency      = 10;
>> cfg.vol            = hdm;
>> cfg.grad           = f.grad;
>> cfg.projectnoise   = 'yes';
>> cfg.lambda         = 5e-28;
>> cfg.method         = 'dics';
>> cfg.feedback       = 'textbar';
>>
>> source = sourceanalysis(cfg,f);
>>
>> then:
>>
>> sd = sourcedescriptives([],source);
>>
>> then:
>>
>> load norm %normalized to MNI brain of single subject
>> sdint = sourceinterpolate([], sd , norm);
>> clear norm
>> %plotting the results
>> cfg.funparameter = 'avg.nai';
>> cfg.anaparameter = 'anatomy';
>> cfg.funcolormap  = 'jet';
>> cfg.method       = 'ortho';
>> cfg.projmethod   = 'nearest';
>> cfg.sphereradius = 20;
>> cfg.surffile     = 'surface_l4_both';
>> figure;
>> sourceplot(cfg,sdint)
>>
>> The result is attached to this email, the gird seems to have moved upwards
>> and somewhat to the front relative to the normalised mri. But it seems to
>> have the right size. I have been playing around with sourceunits mriunits
>> x-y coordinates but nothing helps, or it makes it even worse.
>>
>> Does anybody have an idea what's happening?
>>
>> Yours,
>> Hanneke
>>
>> www.linkedin.com/in/hannekevandijk
>> tel. +49 (0)211 81 13074
>>
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the
>> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
>> and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/neuroimaging/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/neuroimaging/fieldtrip.
>



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The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.