FieldTrip

Flipping dimensions after segmenting the volumes (gray, white, and CSF) can easily introduce offsets. Make sure they are correctly aligned with the anatomical scan. See the following procedure.

The example segmented data is available at ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/beamformer/segmentedmri.mat.

load segmentedmri
 
mri = ft_read_mri('Subject01.mri');
segmentedmri.transform = mri.transform;
segmentedmri.anatomy   = mri.anatomy;
 
figure
cfg = [];
ft_sourceplot(cfg,segmentedmri); %only mri
figure
cfg.funparameter = 'gray';
ft_sourceplot(cfg,segmentedmri); %segmented gray matter on top
figure
cfg.funparameter = 'white';
ft_sourceplot(cfg,segmentedmri); %segmented white matter on top
figure
cfg.funparameter = 'csf';
ft_sourceplot(cfg,segmentedmri); %segmented csf matter on top

When the segmented volumes are not correctly aligned with the anatomical volume, they could look like this.

In this particular example, the volumes are flipped one too many times around the x-axis. In order to solve this, one could flip the image around the x-axis again before preparing the headmodel. For example:

segmentedmri.gray  = flipdim(segmentedmri.gray,1);
segmentedmri.white = flipdim(segmentedmri.white,1);
segmentedmri.csf   = flipdim(segmentedmri.csf,1);