[FieldTrip] Alignment problem in tutorial: Create MNI-aligned grids in individual head-space

Anette Giani anette.giani at tuebingen.mpg.de
Mon Jun 25 14:23:40 CEST 2012

Dear fieldtrip users,


I am running the tutorial: "Create MNI-aligned grids in individual
head-space" (CASE 1). When using the template mri provided on the homepage
(i.e. Subject01.mri), it seems like the grid, the resulting vol and the
anatomy are not aligned. And even worse: besides the misalignment there
seems to be a scaling. Note however, that I am using the exact same
parameter as specified on the homepage. For a better understanding see page
1 of Alignment.pdf attached to this mail.


I found out that things improve when I use the segmentation procedure
specified in the tutorial: "Build a geometrical description of the volume
conduction model of the head" (CASE 2). See page 2 of Alignment.pdf.



In particular, in CASE 1 I do: 


cfg = [];

cfg.downsample  = 2;

cfg.coordsys    = 'ctf';

seg_MNItutorial = ft_volumesegment(cfg, mri);


% plotting case 1

seg_MNItutorial.transform = mri.transform;

seg_MNItutorial.anatomy   = mri.anatomy;


cfg.funparameter = 'gray';

ft_sourceplot(cfg,seg_MNItutorial); %segmented gray matter on top




While, in CASE 2 I do: 


cfg = [];

cfg.write      = 'no';

cfg.coordsys   = 'ctf';

cfg.output     = {'scalp','skull','brain'};

seg_headmodelTutorial   = ft_volumesegment(cfg, mri);


% plotting case 2

mri_combine = mri;

mri_combine.seg  = seg_headmodelTutorial.scalp +
3*seg_headmodelTutorial.skull + 6*seg_headmodelTutorial.brain;

mri_combine.mask = (mri_combine.seg)>0;

cfg = [];

cfg.interactive   = 'yes';

cfg.funparameter  = 'seg';

cfg.funcolormap   = 'jet';

cfg.funcolorlim   = [0 7];

cfg.opacitylim    = [0 1.5];

cfg.maskparameter = 'mask';

figure, ft_sourceplot(cfg,mri_combine);



I am confused, why CASE 2 works, while CASE 1 does not. Could anyone explain
the differences to me? Is doing it like in CASE 2 correct at all?


Thanks a lot in advance!



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