[FieldTrip] source localization difficulties

[Kanal Eliezer]

Thanks for the reply. I'll look into the read_mri issue a bit more myself and see if I can't uncover anything.

>> 
>> Secondly, in an attempt to coregister the MRI and MEG data, I used `ft_determine_coordsys`, which simply opened a window with a picture of three axes (see attached image "ft_determine_coordsys.png"). Shouldn't there be image data overlaid on the axes?
>> 
> 
> There's no figure attached in the mail I got. I would indeed expect to see 3 axes and three intersecting orthogonal slices with anatomical data. That is, if the call to ft_determine_coordsys was ft_determine_coordsys([],mri). Note that this function is just intended to check whether the coordinate system attached to the input data (mri, sensor positions, volume conduction model of the head, source dipole positions etc.) is as expected, or to assign the coordinate system, if you provide some input as to how to interpret the 3 cardinal axes.
> In order to check whether the co-registration went OK I would 
> -co-register the MRI to the coordinate system in which the meg sensors are expressed
> -segment the MRI (these previous 2 steps can be done in freesurfer 
> -create a volume conduction model (let's call it 'vol') of the head (e.g. by calling ft_prepare_singleshell, or even better: call ft_prepare_headmodel with cfg.method = 'singleshell')
> -check the co-registration:  ft_plot_sens(data.grad);hold on;ft_plot_vol(vol), this should show the brain surface and the sensors more or less properly aligned.

Thanks for the overview. Apparently I didn't attach the image. Here it is. There's no slices, just the gridlines. My code is as follows:

% read raw DICOM data
mri 	  = ft_read_mri('raw_data/19/mprage_512x416.5/MR.1.3.12.2.1107.5.2.32.35216.2011051711005397198638928');
mri_coord = ft_determine_coordsys(mri,'interactive','yes');

This may be a bug, as it does seem to work appropriately with data loaded from .mgz files, as well as DICOM data loaded into and then saved out of SPM.

>> 
>> Lastly, I've already segmented and coregistered the MRI and MEG data using FreeSurfer. Is there a way to simply load this data into FieldTrip and get right to plotting the data?
>> 
> 
> Yes, as far as I know ft_read_mri should know how to deal with *.mgz volumes.

Thanks. So, to make sure I get it: to use freesurfer data, I want to load up the .mgz volumes in such a way that I'll end up replicating the output of `ft_volumesegment`. That means finding the .mgz files that represent the `segmentedmri.gray` and `segmentedmri.white` structures and constructing a new structure with the contents of those files.

One last point of confusion: can I actually do MEG-MRI coregistration in FreeSurfer? I've been doing it in MNE, which saves the data to a *.fif file. Is there a way to use the output of the MNE coregistration tool in FieldTrip? I've placed a .mat file with the MNE coregistration data (loaded from the fif file using the MNE `fiff_load_mri` function) online [1] so you can see it's contents; maybe you can tell which field in the structure is the correct transformation matrix.

Thanks!

Elli

[1] http://erikdev.com/mne_coregistration_data.zip

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