strange segmentation w/ ft_volumesegment

Matt F. Panichello panichem at NMR.MGH.HARVARD.EDU
Sat Sep 18 00:53:11 CEST 2010

Hi there,

I am trying to segment an anatomical MRI. Here's the script:

mri = ft_read_mri('test.nii');

%put the mri into the proper orientation
cfg                = [];
mri.anatomy        = permute(mri.anatomy,[1 3 2]);
mri.anatomy        = mri.anatomy(end:-1:1,:,end:-1:1);

%segment the mri
mri = ft_volumerealign(cfg,mri);

cfg.template       = '/spm8/templates/T1.nii';
cfg.coordinates    = 'spm';
cfg.write          = 'yes';           = 'test_segment';
[segmentedmri]     = ft_volumesegment(cfg, mri)

%visualize the results
cfg                = [];
test               = segmentedmri;
test.avg.pow       = test.gray+test.white+test.csf;
test.anatomy       = mri.anatomy;
cfg.funparameter   = 'avg.pow';
cfg.interactive    = 'yes';

No errors are thrown, but when I visualize the results, the segmentation
is clearly incorrect (attached) - it seems to be trying to follow the
contour of the head instead of the brain. I've overlaid both test.nii and
the template in MRIcron and they are aligned and in the same space; is
there any other reason why segmentation may be failing? Thanks in advance!


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