Back to the main page.

Bug 2120 - option to use Nutmeg coreg GUI for fiducial marking and electrode coreg

Reported 2013-04-17 15:05:00 +0200
Modified 2013-04-17 15:23:27 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P3 normal
Assigned to: Johanna
Depends on:
See also:

Johanna - 2013-04-17 15:05:45 +0200

Sarang, Tzvetan and others at Konstanz have an enhancement request. (I discussed this in the FT meeting today, but elaborating here). Some users who use FT for most of the pipeline prefer to use the Nutmeg GUI for easier use of clicking/marking the fiducials and/or for the computation that is computed for alligning Polhemus-marked (or otherwise obtained) electrode positions to the MRI skin surface, and then bringing this allignment into mri.transform, and continuing with analysis in FT from there onwards. Robert suggested that I make a short 2 min video of a demo of this coreg (including audio and the screen). I will ask JM for help on his Mac for this... Sarang has suggested that this be formally incorporated into FT, rather than FT calling NM as an external software. It depends on the SPM MRI viewer. Or could be brought in as a 'nutmeg-lite' into fieldtrip/external/nutmeg. Either way, a separate download of Nutmeg would not be required by the user. A snippet of code, provided by Tzvetan, for after the coreg is done in Nutmeg is as follows: global nuts st mriR=ft_read_mri('yourMRI'); % apply transformation matrix and plot to verify mriR.transform=inv(nuts.coreg.meg2mri_tfm)*st.vols{1}.mat; cfg=[]; cfg.interactive='yes'; figure; ft_sourceplot(cfg, mriR);

Jörn M. Horschig - 2013-04-17 15:23:27 +0200

looking forward to seeing how it's done in nutmeg. I wonder why people are doing it and what's so handy, and wonder even more if it would be better if the FieldTrip UI would be improved to facilitate coregistration rather than relying on 3rd party UIs. I can see the point of sharing algorithms but not so much for incorporating GUIs from other packages, but maybe I'm the only one thinking like that ;)