[FieldTrip] problem with ft_volumerealign and ft_convert_coordsys

[jan-mathijs schoffelen]

Hi Sara,


> 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.
> Any suggestion to solve this?

I don't understand what you mean by 'no results appear on my screen'. Does this mean that mri_realigned is not created?

> 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
> 
> In order to better understand the problem, I have tried to perform a different transformation with the code
> 
> [mri] = ft_convert_coordsys(mri, 'spm', 2)
> and I get the following message
> 
> Converting the coordinate system from ctf to spm
> ??? Undefined function or method 'spm' for input arguments of type 'char'.

You have to have spm on your path in order to get this. try ft_hastoolbox('spm',1) and try again.

> 
> Error in ==> align_ctf2spm at 121
>  switch spm('ver')
> 
> Error in ==> ft_convert_coordsys at 90
>            obj = align_ctf2spm(obj, opt);
> 
> Finally I tried to use the function align_itab2spm in the following way
> mri = align_itab2spm(mri, 2)
> but I get the error message
> 
> ??? Undefined function or method 'spm' for input arguments of type 'char'.
> 
> Error in ==> align_itab2spm at 108
>  switch spm('ver')
> 


See above.

Best,
Jan-Mathijs


> Do you have any idea or suggestion to solve this problem?
> 
> Thanks in advance for any advice,
> Sara
> 
> -------------------------
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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