[FieldTrip] problems with construction of grids for individual subjects

[Maria Rieder]

Dear fieldtrip users,

I have 2 questions regarding the construction of grids for individual 
subjects.

This is the code I used (the template was build according to the 
tutorial "Create MNI-aligned grids..."):

cfg = [];

cfg.write= 'no';

cfg.coordsys= 'ctf';

[segmentedmri] = ft_volumesegment(cfg, mri);

cfg = [];

cfg.method='singleshell';% or single sphere model

vol = ft_prepare_headmodel(cfg, segmentedmri);

cfg = [];

cfg.grid.warpmni= 'yes';

cfg.grid.template= template_grid;

cfg.grid.nonlinear = 'yes'; % use non-linear normalization

cfg.mri= mri;

grid= ft_prepare_sourcemodel(cfg);

1.It turns out that my script works quite well for most of my subjects, 
but in case of one single subject I obtain a curious grid which has no 
grid point in the region of the occipital cortex/cerebellum (2^nd figure 
plotted in red). As you can see in the first figure the subjects mri 
look good and also do the template grid (2^nd figure plotted in green). 
I'm wondering what went wrong. So what options do I have if the 
warping/transform algorithm goes wrong?

2.Why is the template rotated and shifted when comparing it to the 
subjects grid (2^nd figure bottom right)?


Thank you in advance,
Maria

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20121127/88c2ed1d/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: clip_image002.jpg
Type: image/jpeg
Size: 32453 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20121127/88c2ed1d/attachment-0001.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: clip_image003.png
Type: image/png
Size: 171403 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20121127/88c2ed1d/attachment-0001.png>