Coordinate of volume segmentation

MARUYAMA Masaki INSERM masaki.maruyama at CEA.FR
Thu Aug 27 16:29:34 CEST 2009




Would someone please give me suggestions or advices on the coordinate of
volume segmentation? I have struggled with it in these weeks with
referring the examples on the FieldTrip web pages and the previous
discussions on the mailing list. However, my result still seems to be


I realigned a DICOM image file using "volumerealine", and then I
segmented the volume based on the CTF coordinate. Following the examples
on the FieldTrip web pages (e.g,
ce), I examined permutations and flips of the images of segmented
volumes. However, the segmented brain area was partially outside the
head at the best flip (Please see the attached file). The segmented
brain seems to be shifted upward than the real brain position. As far as
I examined, any permutations and flips could not align appropriately. 


Do I need a transformation after the volume segmentation in order to
comensate the difference in the origin between CTF and MNI coordinates?
I'm also wondering if my original MRI image might need to be
permuted/flipped before the volumerealine, since the permutation ([2 3
1]) and the best flip (only x & z axes) in my case are different from
the examples on the web pages.


I would appreciate any responses.



With best regards,

Masaki Maruyama




The following is the script I used.



mri_file = '/neurospin/MRI/DICOM/sbh080102633-0002-00001-000160-01.img';

mri_org = read_mri(mri_file);


cfg = [];

mri = volumerealign(cfg, mri_org);


cfg = [];

cfg.coordinates = 'ctf';

cfg.template    = '/i2bm/platform/spm2/templates/T1.mnc';

[segmentedmri] = volumesegment(cfg, mri);


test = segmentedmri;

test.anatomy = mri.anatomy;

test.transform = mri.transform;


test.gray = permute(segmentedmri.gray, [2 3 1]);

test.white = permute(segmentedmri.white, [2 3 1]);

test.csf = permute(segmentedmri.csf, [2 3 1]);

test.dim = mri.dim;


for t = [1 3]

    test.gray = flipdim(test.gray,t);

    test.white = flipdim(test.white,t);

    test.csf = flipdim(test.csf,t);



test.avg.pow = test.gray + test.white + test.csf;

cfg = [];

cfg.funparameter = 'avg.pow';

cfg.interactive  = 'no';

cfg.method = 'slice';





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