[FieldTrip] Ft_VolumeRealign Shifting Manually Set Fiducials

[Parker]

Hi,


I have a question about MEG anatomical coregistration, particularly when
using ft_volumerealign to do fiducial selection and coregistration
refinement with headshape and ICP.


My current steps with ft_volumerealign are: 1) adding ‘coordsys = neuromag’
field to my mri by manually selecting N,LPA,RPA fiducials 2) refining fit
with cfg.method = 'headshape' and cfg.headshape.icp = 'yes' with the
headshape provided from my MEG file 3) plotting realigned mri to do a
visual check on coordinate system with ft_determine_coordsys. (My code is
also below)


After doing the refinement step, I notice the fiducial positions I
initially set are almost always shifted. I have linked a picture for
example showing 1) coordinates after my fiducial selection, 2) coordinates
after headshape refinement -
https://drive.google.com/drive/folders/13SAOL7FYM2yCiUPTV9StJh1HfNr_hDGP?usp=sharing


In the second image, the nasion is shifted upwards to what I would consider
an incorrect position. (I also noticed that when plotting my source model,
the source points appear to be slightly shifted up compared to one of the
subjects from FT tutorials).


I am guessing the reason why, for ex, my nasion fiducial shift upwards
after headshape refinement is because my headshape variable from my MEG
file has a fiducial field, which are instead the fiducials that are being
used instead of my manually selected ones.


Nevertheless, I was wondering how I could still perform headshape
refinement with ICP and ensure MRI/MEG shape alignment but instead re
select the fiducial positions.


I appreciate the help,

Parker


Step 1 - Fiducial selection

cfg                     = [];

cfg.method               = 'interactive';

cfg.coordsys             = 'neuromag';

cfg.flip                     = 'no';

mri_realigned            = ft_volumerealign(cfg, mri);


Step 2 - headshape refinement

cfg = [];

cfg.method              = 'headshape';

cfg.headshape.headshape = My_MEG_fif_file;

cfg.headshape.icp       = 'yes';

mri_realigned       = ft_volumerealign(cfg,mri_realigned);


Step 3 - Plotting Realigned mri + coordinate system:

cfg = [];

cfg.method              = 'headshape';

shape                   = ft_read_headshape(filename);

shape = ft_convert_units(shape,'mm');



ft_determine_coordsys(mri_realigned, 'interactive', 'no');

hold on;

drawnow;

ft_plot_headshape(shape);
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