[FieldTrip] headmodels

Nugent, Allison C. (NIH/NIMH) [E] nugenta at mail.nih.gov
Fri Feb 15 18:34:44 CET 2013

It certainly works with the unit conversions in the version I'm currently using, which is from 2/5/2013 - - thanks so much!!  As soon as I have a chance, I'll download the latest version to test.

Thanks again!

Allison Nugent, PhD
MRI Physicist
Experimental Therapeutics and Pathophysiology Branch
Ph. 301-451-8863
nugenta at mail.nih.gov

From: "Jörn M. Horschig" [mailto:jm.horschig at donders.ru.nl]
Sent: Friday, February 15, 2013 11:56 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] headmodels

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:


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
[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:

cfg=[]; cfg.method='singleshell';
ft_plot_vol(vol_realistic);hold on

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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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<mailto: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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