Coordinate of volume segmentation

[MARUYAMA Masaki INSERM]

Hello,

 

 

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
incorrect.

 

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,
http://fieldtrip.fcdonders.nl/example/read_neuromag_mri_and_create_singl
e-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_spa
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);

end

    

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

cfg = [];

cfg.funparameter = 'avg.pow';

cfg.interactive  = 'no';

cfg.method = 'slice';

figure(2);clf

sourceplot(cfg,test)

 

 


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