Incorrect coordinates?

Jared Van Snellenberg jaredvs at GMAIL.COM
Tue Oct 10 22:38:53 CEST 2006


Hi there,

I've been analyzing the output of BESA's multiple source beamformer (MEG 
data) using Fieldtrip, and it appears that there is a problem with the 
coordinate system. The results of volumewrite, when overlayed with the spm 
T1.img, appear to be substantially outside of the brain, and in oddly 
shaped patterns that suggest an error in assigning statical values to the 
correct coordinates.

The analysis protocol used was as follows (we only had MRI's for 2 
subjects, one of these was used for all subject who did not have MRI's--for 
convenience I simply use one mri for all subjects in the example below):

mri=read_fcdc_mri('mri.img');

fdir=pwd;

files=dir([fdir filesep '*.dat']); %these are the BESA .dat files

sinterp_cfg.interpmethod='cubic';
sinterp_cfg.sourceunits='mm';

norm_cfg.template=which('T1.mnc');
norm_cfg.parameter='all';
norm_cfg.coordinates='spm';
norm_cfg.name='high_alpha_beamformer_normed';

for k=1:length(files)
    src(k)=besa2fieldtrip([fdir filesep files(k).name]);
    interp(k)=sourceinterpolate(sinterp_cfg,src(k),mri);
    volume(k)=volumenormalise(norm_cfg,interp(k));
end

grav_cfg.parameter='pow';
grav_cfg.keepindividual='yes';

grandavg=sourcegrandaverage(grav_cfg,volume(1),volume(2),volume(3),volume
(4),volume(5),volume(6),volume(7),volume(8),volume(9),volume(10),volume
(11),volume(12));

stat_cfg.parameter='pow';
stat_cfg.method='parametric';
stat_cfg.statistic = 'zero-baseline';
stat_cfg.bonferoni = 'no';
stat_cfg.threshold=0.01;

stat=sourcestatistics_parametric(stat_cfg,grandavg);

write_cfg.parameter='tscore';
write_cfg.filename='alpha';
write_cfg.filetype='spm';
write_cfg.coordinates='spm';
write_cfg.scaling='no';

volumewrite(write_cfg,stat)


When I overlay the .img on the MNI T1.img using MRICro, there's a lot of 
data outside of the brain.

Any suggestions as to where something may have gone wrong would be greatly 
appreciated. I would happily provide the resulting alpha.img and alpha.hdr, 
though as the .img is 55MB I won't attach it to this message.

Thanks very much,

Jared Van Snellenberg
Social Cognitive Affective Neuroscience Unit
http://scan.psych.columbia.edu
(212) 854-7858 p 
(212) 854-3609 f
Department of Psychology, Columbia University
406 Schermerhorn Hall
1190 Amsterdam Avenue, Mail Code 5501
New York, NY 10027



More information about the fieldtrip mailing list