[FieldTrip] Ft_VolumeRealign Shifting Manually Set Fiducials

[Parker]

I appreciate your feedback. Given that my manually selected fiducials don't
agree with the ones stored in the MEG headshape variable (which were set up
before by the researcher prior to running the scan), is it acceptable to
first modify the headshape variable by removing the fiducial field prior to
inputting it into the ft_voluemrealign function to use ICP.

(I understand ICP would benefit from more headshape points but I notice it
still works well and that ICP does not seem like the source of the issue
here but rather just the disagreeing fiducials.)

Thank you again!

On Mon, Jul 8, 2024 at 9:22 PM Parker <pjosephsmith6791 at gmail.com> wrote:

> 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);
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20240726/774bc2d4/attachment.htm>