[FieldTrip] Coregistration using fixed fiducials coordinates

[Rasha Haider]

Dear Jörn,
thank you for your reply, actually I didn't send many emails because I didn't receive any reply directly, the problem was that each time I sent the email I received a failure email mentioning that my email was not delivered so I had to resent it again. My apologies for this I don't know what was the problem. 

I will follow your advise hoping to get some results.
Regards
Rasha



________________________________
 From: Jörn M. Horschig <jm.horschig at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl> 
Sent: Tuesday, July 8, 2014 4:00 PM
Subject: Re: [FieldTrip] Coregistration using fixed fiducials coordinates
 

Hi Rasha,

you can call ft_determine_coordsys, or set the field manually if you 
what coordinate system the MRI is in.

You could have also used the search function of the fieldtrip wiki (on 
the upper right on the page), e.g. by searching for coordinate system:
http://fieldtrip.fcdonders.nl/?do=search&id=coordinate+system
This leads to a page that lists all pages on which the term coordinate 
system occur. You can see that the first match links to a FAQ, which 
also hints to ft_determine_coordsys. FAQs can also be found when 
navigating to "User documentation" and then "Frequently asked 
questions". We spent quite some time to list a number of questions and 
detailled answers there. The answers are mostly more extensive than the 
question alone, so any question that might be remotely related to your 
actual question might be of interest there.

However, please don't be afraid to ask any further questions, just 
notice that we're all doing this here besides our research, so sometimes 
it might take a bit longer for us to respond than within a few hours. 
Any search that you do in advance on the FT wiki is time that we do not 
have to spend ;) So, please don't send the same message five times 
within not even a week, once a week should be enough ;)

Best,
Jörn


On 7/8/2014 6:44 AM, Rasha Haider wrote:
> Dear fieldtrip experts,
> Im trying to do source localization for simulated EEG data, for this I 
> followed the tutorial in page:
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> I was trying to use the mri image provided by fieldtrip 
> (Subject01.mri) and EEG template (standard_1020.elc) in my work.
> The mri image need to be re-aliened to the Talairach space for 
> coregistration with EEG space. In the tutorial you use 
> (ft_volumerealien) to do that using interactive method.
> I have two questions:
>
> First, how can I do the coregistration using fixed coordinates of the 
> 3 fiducials (nasion, left pr, right pr), in other words how can I get 
> the coordinates of the fiducials in both Talairach and EEG spaces to 
> do the coregistration using the script only not manually.
>
> Second, I tried to use the mri image provided by the spm toolbox 
> because its already aliened to Talairach space, but when I try to do 
> segmentation I get error that coordinates field does not exist:
>
> ??? Reference to non-existent field 'coordsys'.
>
> Error in ==> ft_volumesegment at 284
>   original.coordsys  = mri.coordsys;
>
> Error in ==> segmentation_spm_mri at 24
> seg           = ft_volumesegment(cfg, mrirs);
>
> I read the image using (ft_read_mri) function, I don't find the field 
> specified for the coordinates:
>
> disp(mri)
>           dim: [177 240 256]
>       anatomy: [177x240x256 double]
>           hdr: [1x1 struct]
>     transform: [4x4 double]
>          unit: 'mm'
>
> How can I solve this problem so I can use the mri image in SPM for 
> further analysing in fieldtrip?
>
> Sorry for the long email I would be thankful for any help.
> Regards
> Rasha
>
>
>
>
> _______________________________________________
> 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

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