[FieldTrip] headmodels

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Fri Feb 15 17:55:51 CET 2013

Dear Allison,

I was encountering similar issues the last two days and hope to have 
fixed some unit conversion bugs. Thus it might be that with the newest 
FT version, you don't need to manually convert the units anymore as JM 
suggested. Could you give it a try for me and see whether it works 
without JMs manual approach in the newest FT version?


On 2/15/2013 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 MRIthat 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 <mailto:nugenta at mail.nih.gov>
> _______________________________________________
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> fieldtrip at donders.ru.nl
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Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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