[FieldTrip] headmodels

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Fri Feb 15 16:16:52 CET 2013

Hi Allison,

The warning you get is inconsequential and will be fixed soon.

Regarding the scale of the data objects, you can use ft_convert_units to get them all in the same scale:

hdr.grad = ft_convert_units(hdr.grad); % tries to add a unit field if it does not exist
vol = ft_convert_units(vol, hdr.grad.unit);

Then you can proceed with the plotting.


On Feb 15, 2013, at 3:51 PM, Nugent, Allison C. (NIH/NIMH) [E] wrote:

> Hello,  I’m very sorry to repost this, but I’m hoping that someone might be able to give me advice.
> I have an MRI in nifti format.  It has already been re-aligned with the fiducial markers.   I’ve scoured the tutorials, but most seem to deal with MRIs that are already in the ctf coordinate system. 
> I’ve imported the MRI like so:
> mri=ft_read_mri(‘ABC_ortho_anat.nii’);
> mri=ft_determine_coordsys(mri)
> I re-label the coordinate axes, and set the origin – when it’s done, it has “Neuromag” as the coordsys, although that’s not how it was created.  Next:
> cfg=[]; cfg.method=’interactive’
> mri_realigned=ft_volumerealign(cfg,mri)                             % to set the fiducial points
> cfg=[];
> [segmentedmri]=ft_volumesegment(cfg, mri_realigned)
> During execution I get this warning:
> Warning: could not open /tmp/tpe3eb8b07_40e0_49bf_88d2_e0c227c3d7af.img 
> Even though the file appears to exist – and the program completes and produces a segmented MRI that looks fine.  Finally:
> hdr=ft_read_header(‘ACN.ds’);
> cfg=[]; cfg.method=’singleshell’;
> vol_realistic=ft_prepare_headmodel(cfg,segmentedmri);
> figure
> ft_plot_vol(vol_realistic);hold on
> ft_plot_sens(hdr.grad)
> The plot has the sensor array and the headmodel on different scales – like it didn’t properly adjust for the difference in mm and cm, even though the units are specified in the data structures.   I’d ultimately also like to be able to use the localspheres model, and compare results, but since I can’t figure out how to plot that headmodel to check it, I thought I’d start with one that I can plot. 
> Thank you!
> Allison Nugent, PhD
> MRI Physicist
> Experimental Therapeutics and Pathophysiology Branch
> Ph. 301-451-8863
> nugenta at mail.nih.gov
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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