O sorry, I made I typo I see. My reply was what I remembered from some time ago ;-)
It should be inv(mat)\[1 1 1 0]' otherwise you will incorporate the translation parameters...
Just checked on a few images, and the above works for me. Notice that the order of the voxel size you get is according to voxel space. That is, when you scan saggittally, the first number will be the slice thickness (from ear to ear).
Cheers,
Bas
Op 25-11-11 13:47, han zhang schreef:Dear Bas,I followed your suggestion using inv(mat)\[1 1 1 1], but the output was a 4*1 vector, containing numbers that coundn't be voxel size:[219-156191]
What's wrong with my script?Han2011/11/25 S.F.W. Neggers <[log in to unmask]>
No this is not wrong, both SPM and MRicron are right. The diagonol is NOT necessarily equal to the voxel size (it only is for an image without any angulation). This matrix is a so called 4D affine transormation matrix, constituting the voxel-to-world matrix in the Nifti specification from NIH. Don't try to interpret it when you do not know what is represents, 4D linear algebra is not for the faint at heart ;-). See http://nifti.nimh.nih.gov/nifti-1 for more information on the nii specs.
When applying a rotation matrix to the original matrix, the diagonal changes, and this is correct behavior (check your linear algebra textbooks). When you open your image in spm, the right window will compute and display the voxel size for you. This does not change after realignment.
When you want to compute it yourself do:
V=spm_vol(spm_select);
inv(V.mat)\[1 1 1 1]'
Good luck,
Bas
Op 25-11-11 10:56, han zhang schreef:Hi Helen,This problem is also bothering me. The voxel size as indicated in the diagnal of the MAT matrix was sometimes not in concordance with MRIcron (as seen from image 'information' on the menu of MRIcron).For example, my MAT matrix of a head-motion-corrected nifti image is :-3.4124 0 -0.72 223-0.033 3.4263 0.4806 -159-0.42 -0.27 5.94 14.7The voxel size should be 3.4124* 3.4263*5.94?However, MRIcron reported it as 3.5*3.5*7, quite different Huh?What I thought is that, maybe after realignment (motion correction with rigid body transformation), the MAT file had been changed, not as diagnal as it should be before. So the voxel size should not be taken from the diagnal number of the MAT file. Am I right?Han
2011/11/25 Helen Beaumont <[log in to unmask]>
Help please.
I am writing a Matlab matrix (read from a Phillips ParRec file) out as nii data.
The voxel size is 3.5 x 3.5 x 5.95 mm, 64 x 64 x 20 matrix.
N.mat is
3.5000 0 0 -113.7500
0 3.5000 0 -113.7500
0 0 5.9500 -62.4750
0 0 0 1.0000
When I use SPM to display it, the voxel size is OK, and origin is close to AC.
However, if I use MRIcroN with “re-orient on load” box checked in preferences,
voxel size is 1 x 1 x 1 mm, and origin is bottom L corner.
Helen Beaumont
ISBE
University of Manchester
Stopford Building, Oxford Rd
Manchester M13 9PT
Tel: 0161 275 1259
--
Han ZHANG
http://publicationslist.org/han_zhang
Center for Cognition and Brain Disorder, Hangzhou Normal UniversityAddr: 7th Bldg, Affil Hosp of Hangzhou Normal Univ, Wenzhou Rd 126#, Hangzhou 310015Fax/Tel: +86-0571-88285651Mobile Tel: 15869174768-- -------------------------------------------------- Dr. S.F.W. Neggers Division of Brain Research Rudolf Magnus Institute for Neuroscience Utrecht University Medical Center Visiting : Heidelberglaan 100, 3584 CX Utrecht Room B.01.1.03 Mail : Huispost B01.206, P.O. Box 85500 3508 GA Utrecht, the Netherlands Tel : +31 (0)88 7559609 Fax : +31 (0)88 7555443 E-mail : [log in to unmask] Web : http://www.neuromri.nl/people/bas-neggers : http://www.neuralnavigator.com (CEO) --------------------------------------------------
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Han ZHANG
http://publicationslist.org/han_zhang
Center for Cognition and Brain Disorder, Hangzhou Normal UniversityAddr: 7th Bldg, Affil Hosp of Hangzhou Normal Univ, Wenzhou Rd 126#, Hangzhou 310015Fax/Tel: +86-0571-88285651Mobile Tel: 15869174768-- -------------------------------------------------- Dr. S.F.W. Neggers Division of Brain Research Rudolf Magnus Institute for Neuroscience Utrecht University Medical Center Visiting : Heidelberglaan 100, 3584 CX Utrecht Room B.01.1.03 Mail : Huispost B01.206, P.O. Box 85500 3508 GA Utrecht, the Netherlands Tel : +31 (0)88 7559609 Fax : +31 (0)88 7555443 E-mail : [log in to unmask] Web : http://www.neuromri.nl/people/bas-neggers : http://www.neuralnavigator.com (CEO) --------------------------------------------------