[FieldTrip] headmodels

[Nugent, Allison C. (NIH/NIMH) [E]]

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
NIMH/NIH/DHHS
Ph. 301-451-8863
nugenta at mail.nih.gov<mailto:nugenta at mail.nih.gov>


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