[FieldTrip] Fiducial registration issue

[Schoffelen, J.M. (Jan Mathijs)]

Hi Alex,

The ‘fiducial’ method in ft_volumerealign assumes the fiducials’ locations to be expressed in voxel-coordinates. Are you sure that this is the case for the data that you are using? If so, then it is important to know that the call to ft_volumereslice changes the voxel-coordinate system, which invalidates the earlier defined fiducials (in voxel space).

So: two possible causes:
1) the fiducials D2.datareg.fid_eeg.pnt are not expressed in voxel coordinates, or
2) the reslicing causes a shift in the voxel coordinates

Best wishes,
Jan-Mathijs


On 7 Jun 2024, at 18:36, Alex Williams via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello Fieldtrip community,

  I was curious if anyone here has come across this issue. I'm currently in the process of registering fiducials to a participant from the CamCan study. The meeg data, D, I'm using has been converted from SPM to fieldtrip using the function. spm2fieldtrip(). The converted data itself has been defined, and has undergone pre-processing and time-locking in SPM. ft_read_mri() used a .nifti MRI file and an empty configuration. I have used the fiducials applied to the segmented mri model's configuration and subsequently used the configuration to realign the segmented mri using ft_volumerealign() with cfg.coordsys='neuromag'. After, segmentation was done using ft_volumesegment(), again with an empty configuration. However, it seems as though the gradiometer array and the headmodel aren't properly aligned to one another after plotting both. The unit of the grad, mri and headmodel are all in 'mm'.

%% Sensors

grad = ft_read_sens([Path1,Path2], 'senstype', 'meg');
%% MRI Read

mri = ft_read_mri([Path1,Path3]);
%% Reslice Volume

cfg = [];
cfg.resolution = 1;
mri = ft_volumereslice(cfg, mri);
%% Realign Coord Sys.

cfg=[];
cfg.fiducial.nas = D2.datareg.fid_eeg.fid.pnt(1,:);
cfg.fiducial.lpa = D2.datareg.fid_eeg.fid.pnt(2,:);
cfg.fiducial.rpa = D2.datareg.fid_eeg.fid.pnt(3,:);
nas=cfg.fiducial.nas;
lpa=cfg.fiducial.lpa;
rpa=cfg.fiducial.rpa;
cfg.coordsys='neuromag';
cfg.method='fiducial';
mri = ft_volumerealign(cfg, mri);
ft_sourceplot([],mri)

-Alex
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd1373dc7d8014be6541208dc87af3fa5%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638534433957286467%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=07o6EQH8ZzPiWiqVGljqtCFmgfhcA53ZH8RzdnOqqRw%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20240608/614270d4/attachment.htm>