[FieldTrip] fit volume segment and sensors

Tue Jan 21 18:15:22 CET 2014

Dear Jörn, dear Fieldtrippers,

I have downloaded the 20140114 version of Fieldtrip and tried again to
use the command ft_volumerealign in the following way (as suggested in  
the tutorials)

mri =  ft_read_mri('*....\Subject01.mri');
cfg=[];
cfg.method = 'interactive';
mri_realigned = ft_volumerealign(cfg, mri);

Then I identify it by pressing either n/l/r for fiducials and finally
I press q in order to quit.
But no results appear on my screen.

I have tried to use also the following command
   [mri] = ft_convert_coordsys(mri, 'itab');

but I get the error message
  [mri] = ft_convert_coordsys(mri, 'itab');
??? Error using ==> ft_convert_coordsys at 102
conversion from ctf to itab is not yet supported

There is also a command ft_transform_geometry. But this asks for a
transformation matrix that is created by using ft_volumerealign. So I
cannot use it at the moment.

Any idea or suggestion to solve this problem? Maybe there is something  
I am missing?

> Dear Sara,
>
> the procedure described on the FT-page is tailored towards data
> gathered from CTF data just because we happen to have a CTF-system
> here. Since you have itab-data, the coordinate system of your sensors
> (gradiometers) is not in ctf-space. Some more information on the
> different coordinate systems can be found here:
> http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined?s[]=coordinate&s[]=system#details_of_the_chieti_itab_coordinate_system
>
> Your first step needs to be to coregister the gradiometer information
> with the MRI. Afaik, ft_volumerealign will then also take care of the
> coordinate system then (or, more precisely, return the appropriate
> transformation). See also here
> http://fieldtrip.fcdonders.nl/faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions?s[]=coordinate&s[]=system
>
> If I remember correctly, this will not change the coordinate system of
> the gradiometers, but adjust the transformation matrix of the MRI
> instead. You do not need to be in CTF-space, you just need to make sure
> that all your data are in the same coordinate-system. Once you got
> that, it should work.  For example, for EEG source reconstruction you
> can stay in MNI-space all the time. Dealing with these transformation
> between coordinate systems is some nasty job, so take care you do it
> correctly and e.g. not get confused by neurological and radiological
> convention
> And note that there is also ft_convert_coordsys for transformation, but
> I am not sure whether that works for gradiometers, yet. I think this
> all just works for volumes. I hope this works for you.
>
> Best,
> Jörn
>
> s.rombetto at cib.na.cnr.it wrote:
>> Dear Fieldtrippers
>>
>> I 'm trying to perform source analysis on MEG data.
>> I use an AtB system (usually it is described as 'itab' in fieldtrip)
>>
>> First I have preprocessed my data and I have calculated the cross    
>> spectral density matrix
>>
>> Then I have constructed the forward model
>>
>> mri = ft_read_mri('Subject01.mri');
>> cfg = [];
>> cfg.write      = 'no';
>> cfg.coordsys   = 'ctf';
>> [segmentedmri] = ft_volumesegment(cfg, mri);
>>
>> and segmented the brain surface:
>>
>> cfg = [];
>> cfg.method = 'singleshell';
>> vol = ft_prepare_headmodel(cfg, segmentedmri);
>>
>> With the command ft_read_sens I have also read the sensors positions.
>>
>> Before going on I have checked the results plotting the volume and   
>>  the sensors using the commands
>> vol = ft_convert_units(vol,'cm');
>> sens = ft_read_sens(rawdataname);
>> figure
>> ft_plot_sens(sens, 'style', '*b');
>> hold on
>> ft_plot_vol(vol);
>>
>> and I have noticed that the result is wrong because the volume    
>> soesn't fit the sensors as shown in the attachment
>> Moreover, following some topics in the mailing list I have used
>>
>> ft_determine_coordsys(mri)
>> ft_determine_coordsys(vol)
>> ft_determine_coordsys(sens)
>>
>> and I have found that the coordinate systems are diffeerent.
>>
>> As far as I understand I should use the ctf coordinate system to    
>> perform the source analysis. But even if I try to specify this    
>> coordinate system it did not work.
>> Any suggestion to solve this problem?
>>
>> Kind regards
>> -------------------------
>> Dott.ssa Sara Rombetto
>> Istituto di Cibernetica
>> "E. Caianiello"
>> Via Campi Flegrei, 34
>> 80078 Pozzuoli (NA)
>> Italy
>> mob +39 3401689815
>> tel +39 0818675361
>> fax +39 0818675128
>> --------------------------
>> "I disapprove of what you say, but I will defend to the death your   
>>  right to say
>> it." [Evelyn Beatrice Hall, The Friends Of Voltaire]
>>
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>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-------------------------
   Dott.ssa Sara Rombetto
   Istituto di Cibernetica
   "E. Caianiello"
   Via Campi Flegrei, 34
   80078 Pozzuoli (NA)
   Italy
   mob +39 3401689815
   tel +39 0818675361
   fax +39 0818675128
--------------------------
"I disapprove of what you say, but I will defend to the death your
right to say
it." [Evelyn Beatrice Hall, The Friends Of Voltaire]

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