[FieldTrip] leadfields MNI-coordinates

[Pelt, S. van (Stan)]

Hi Barbara,

Your code actually looks fine to me. Some things that I could think of:



1.       Did you specify cfg.coordinates=’mni’ before applying ft_volumenormalise?



2.       Did you select the right volumes for plotting? So


a.         For CTF head space:
    % make a figure of the single subject headmodel
    cfg=[];
    cfg.location=ctfpos(i,:);
    cfg.locationcoordinates='head';
    ft_sourceplot(cfg,mri_realign)


b.      And for MNI-space:
cfg=[];
cfg.location=targets(i,:);
cfg.locationcoordinates='head';
ft_sourceplot(cfg,mri_realign_mni)

This should lead to the same anatomical locations.

Hope this helps!

Stan

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Barbara Haendel
Sent: vrijdag 15 mei 2015 10:27
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] leadfields MNI-coordinates

Hi there,
I found this very nice thread on warping between spm and ctf space (thanks Jan-Mathijs and Stan) and at first sight it seems to work fine (numbers match after applying warping back and forth) but when I try to navigate to the spot in the plotted figure the point of interest seems not to be the same.

mri_realign_mni=ft_volumenormalise([],mri_realign)
% Inverse warping
mnipos=[-48 -75 8]; % [46 -78 6]; MT
posback=ft_warp_apply(mri_realign_mni.params,mnipos,'sn2individual')
ctfpos= ft_warp_apply(pinv(mri_realign_mni.initial),posback)

 -8.6110   55.6190   50.0473

I plotted either  (see .jpg)

A.    the source (source = ft_sourceanalysis(cfg, freq));
B.    the interpolated source (sourceInt  = ft_sourceinterpolate(cfg, source , mri_realign);
C.    the normalized source (sourceIntNorm = ft_volumenormalise(cfg, sourceInt);

and manually navigated to the respective coordinates. While for the normalized source the location makes sense (area MT) the location for A and B seems different.

Is there any obvious mistake I’m overlooking?

Thanks a lot!
Barbara



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