[FieldTrip] Source Reconstruction

[Ainsley Temudo]

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
Mobile (UAE): +971 56 664 6952

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