[FieldTrip] Source Reconstruction

Wed Mar 8 10:36:22 CET 2017

Hi Jan-Mathijs,
I managed to get the ft_electoderealign to work after some debugging, which
involved commenting out parts of the script. Could you take a look at the
two images I've attached. The first is my volume conduction model and the
sensors before realignment (unaligned.fig) and the second is after
realignment (aligned.fig).
any idea why the MRI markers which were used as the template (green) are so
far apart from the MEG marker coil positions( red)? also it seems that
before realignment everything looks okay, but how is that possible if my
volume conduction model is in CTF and my MEG sensors are not?
thanks
Ainsley

On Wed, Mar 8, 2017 at 12:15 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Ainsley,
>
> I have never worked with ‘yokogawa’ data myself, so I can’t be of much
> help. The documentation you point to is already several years old, and
> appears not to have been actively maintained. Most likely the error you get
> is caused by incompatibility between the current version of the FieldTrip
> code, and the example code provided. Perhaps someone that has recently done
> coregistration between anatomical data and yokogawa data can chime in?
>
> Best wishes,
> Jan-Mathijs
>
>
>
> On 08 Mar 2017, at 09:03, Ainsley Temudo <ainsley.temudo at nyu.edu> wrote:
>
> Hi Jan-Mathijs
> Thanks for getting back to me so quickly. I originally used
> Ft_sensoralign, but I got the error messages one of which said
> 'FT_SENSORREALIGN is deprecated, please use FT_ELECTRODEREALIGN instead'
> so thats why I used electrode realign instead, even though it's MEG data.
>
> I've been following this page to do the realignment.
>
> http://www.fieldtriptoolbox.org/getting_started/yokogawa?s[]=yokogawa
>
> if I use sensorrealign how should I deal with these error messages?
>
> Undefined function or variable 'lab'.
>
> Error in channelposition (line 314)
> n   = size(lab,2);
>
> Error in ft_datatype_sens (line 328)
>         [chanpos, chanori, lab] = channelposition(sens);
>
> Error in ft_sensorrealign (line 212)
> elec_original = ft_datatype_sens(elec_original); % ensure up-to-date
> sensor description (Oct 2011)
>
>
> is there another way to realign my anatomical with my MEG sensors without
> using ft_sensorrealign?
>
> Thanks,
> Ainsley
>
> On Wed, Mar 8, 2017 at 11:26 AM, Schoffelen, J.M. (Jan Mathijs) <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Ainsley,
>>
>> Why would you want to use sensorrealign/electroderealign since you have
>> MEG-data? The former functions may be needed for EEG electrodes, not for
>> MEG sensors.
>>
>> Best wishes,
>> Jan-Mathijs
>>
>>
>> J.M.Schoffelen, MD PhD
>> Senior Researcher, VIDI-fellow - PI, language in interaction
>> Telephone: +31-24-3614793 <+31%2024%20361%204793>
>> Physical location: room 00.028
>> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>>
>>
>> On 08 Mar 2017, at 07:52, Ainsley Temudo <ainsley.temudo at nyu.edu> wrote:
>>
>> Hi FieldTrip Experts,
>>
>> I am trying to perform source reconstruction, and I am having trouble
>> with coregistering my anatomical with the sensors. The MEG system we're
>> using is Yokogawa and the anatomical is a NIFTI file. I get some errors
>> when using  ft_sensorrealign and ft_electroderealign. I will go through the
>> steps I took before getting to this stage, as maybe I have done something
>> wrong.
>>
>> first I read in my MRI and determine the coordinate system which is LPS.
>>
>> mriunknown = ft_read_mri('WMCP1011+22+t1mprage.nii');
>> mri = ft_determine_coordsys(mriunknown, 'interactive','yes')
>>
>>  next I realign to the CTF coordinate system by marking the NAS LPA, RPA
>>
>> cfg = [];
>> cfg.method = 'interactive';
>> cfg.coordsys = 'ctf';
>>
>> mri_ctf = ft_volumerealign(cfg, mir);
>>
>> I read in the sensor information and added in the coordinates for the
>> marker positions. we have five marker positions, the three I picked were
>> the left and right ear markers and the middle forehead marker.
>>
>> grad=ft_read_sens('srcLocTest01_FT_01.con');
>>
>>
>> grad.fid.pnt(1,:) = [96.07 3.11 -5.32]./10;
>> grad.fid.pnt(2,:) = [11.13 75.50 -78.23]./10;
>> grad.fid.pnt(3,:) = [8.50 -75.09 -64.60]./10;
>>
>> grad.fid.label = {'NAS' 'LPA' 'RPA'};
>>
>> I then put the template marker point cordinates  into the configuration
>> which were taken from the mri_ctf
>>
>> cfg = [];
>> cfg.method = 'fiducial';
>> cfg.target.pnt(1,:) = [91.1 3.0 49.2]./10;
>> cfg.target.pnt(2,:) = [-0.1 70.5 0.0]./10;
>> cfg.target.pnt(3,:) = [0.1 -70.5 0.0]./10;
>>
>> cfg.target.label = {'NAS' 'LPA' 'RPA'};
>>
>>
>> grad_aligned = ft_sensorrealign(cfg, grad);
>>
>> when I use ft_sensorrealign I get the following errors  :
>>
>> Undefined function or variable 'lab'.
>>
>> Error in channelposition (line 314)
>> n   = size(lab,2);
>>
>> Error in ft_datatype_sens (line 328)
>>         [chanpos, chanori, lab] = channelposition(sens);
>>
>> Error in ft_sensorrealign (line 212)
>> elec_original = ft_datatype_sens(elec_original); % ensure up-to-date
>> sensor description (Oct 2011)
>>
>>
>> when I use ft_electroderealign I get the following errors:
>>
>> Error using ft_fetch_sens (line 192)
>> no electrodes or gradiometers specified.
>>
>> Error in ft_electroderealign (line 195)
>>   elec_original = ft_fetch_sens(cfg);
>>
>>
>> Hope you can help me figure out why I'm getting these errors.
>> Thanks,
>> Ainsley
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>>
>> J.M.Schoffelen, MD PhD
>> Senior Researcher, VIDI-fellow - PI, language in interaction
>> Telephone: +31-24-3614793 <+31%2024%20361%204793>
>> Physical location: room 00.028
>> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> *Ainsley Temudo*
> Research Assistant
> Sreenivasan Lab
> NYU Abu Dhabi
> Office Tel (UAE): +971 2 628 4764 <+971%202%20628%204764>
> Mobile (UAE): +971 56 664 6952 <+971%2056%20664%206952>
>
> NYU Abu Dhabi, Saadiyat Campus
> P.O. Box 129188
> Abu Dhabi, United Arab Emirates
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>

-- 
*Ainsley Temudo*
Research Assistant
Sreenivasan Lab
NYU Abu Dhabi
Office Tel (UAE): +971 2 628 4764
Mobile (UAE): +971 56 664 6952

NYU Abu Dhabi, Saadiyat Campus
P.O. Box 129188
Abu Dhabi, United Arab Emirates
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