[FieldTrip] Aligning Electrodes

[Julian Keil]

Hi Isaiah,

so you are having trouble using your own MRI, right? Have you tried the example-MRI that comes with the tutorial or the standard mri found in the templates-folder?
Depending on your MRI-machine you might not actually get any header info (which is stored in .hdr). For example, with the Simens Verio which I use here, I get DICOM files which contain a .hdr when read into field trip, however the .hdr field does not contain any information on the fiducials.

So, in order to realign your EEG-Electrodes and the MRI without the fiducials, you need to use the ft_electroderealign-function with cfg.method = interactive.
You also need to take some steps before that, i.e. you need to realign your MRI (ft_volumerealign), segment the MRI (ft_volumesegment) and create a head model (ft_prepare_headmodel).
From your plot I guess that you already have the head model and EEG-Electrodes, so you can use the code from the example script (http://fieldtrip.fcdonders.nl/example/align_eeg_electrode_positions_to_bem_headmodel):

% align interactive to surface of headmodel stored in vol.bnd
cfg = [];
cfg.method    = 'interactive';
cfg.elec      = elec;
cfg.headshape = vol.bnd(1);
elec_new = ft_electroderealign(cfg);
Good luck, in case you're still having trouble I can also send you a copy of my personal script I use to create head models.

Julian

Am 20.08.2014 um 21:55 schrieb Isaiah C. Smith:

> Hello Julian,
> 
> Thanks for the help. I am using MATLAB 2014a, and I am using my own mri, and locations. FieldTrip is up to date as well. The result is below.<Screen Shot 2014-08-20 at 12.48.14 PM.png>
> I am trying to move the electrodes slightly. 
> 
> When I follow the steps on the website.
> >> disp(mri.hdr.fiducial.mri)
> Reference to non-existent field 'HDR'.
> 
> Isaiah
> On Aug 19, 2014, at 1:26 AM, Julian Keil <julian.keil at gmail.com> wrote:
> 
>> Hi Isaiah,
>> 
>> could you check which FT-Version & Matlab-Version you are using?
>> I just checked it and it seems to work fine (on Matlab 2011b).
>> Also, could you post the output from calling "mri" and "mri.hdr"?
>> 
>> Good luck
>> 
>> Julian
>> 
>> ********************
>> Dr. Julian Keil
>> 
>> AG Multisensorische Integration
>> Psychiatrische Universitätsklinik
>> der Charité im St. Hedwig-Krankenhaus
>> Große Hamburger Straße 5-11, Raum E 307
>> 10115 Berlin
>> 
>> Telefon: +49-30-2311-1879
>> Fax:        +49-30-2311-2209 
>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>> 
>> Am 18.08.2014 um 23:52 schrieb Isaiah C. Smith:
>> 
>>> Hello,
>>> 
>>> I am trying to realign the electrodes that I have, and I am going along with the cook book, but I keep getting an error.
>>> 
>>> mri = ft_read_mri('Subject01.mri');
>>> 
>>> disp(mri.hdr.fiducial.mri)
>>>     nas: [87 60 116]
>>>     lpa: [29 145 155]
>>>     rpa: [144 142 158]
>>> Reference to non-existent field 'hdr'.
>>> 
>>> I cannot display. Am I missing a prior step?
>>> 
>>> Best,
>>> Isaiah Smith
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
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