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Hi all, I try this time in my way, to orthogonize mat matrix, I use: [U S V] = svd(head.mat(1:3, 1:3)), and S give me the voxel size. Hope it helps for other guys. Han 2011/11/25 S.F.W. Neggers <[log in to unmask]> > ** > 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 > -156 > 19 > 1] > > What's wrong with my script? > Han > > > > 2011/11/25 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 14.7 >> >> The 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 University >> Addr: 7th Bldg, Affil Hosp of Hangzhou Normal Univ, Wenzhou Rd 126#, >> Hangzhou 310015 >> Fax/Tel: +86-0571-88285651 >> Mobile 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) >> -------------------------------------------------- >> >> ------------------------------ >> >> *De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht >> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender >> direct te informeren door het bericht te retourneren. Het Universitair >> Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin >> van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat >> geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. >> 30244197. * >> >> *Denk s.v.p aan het milieu voor u deze e-mail afdrukt. * >> ------------------------------ >> >> *This message may contain confidential information and is intended >> exclusively for the addressee. If you receive this message unintentionally, >> please do not use the contents but notify the sender immediately by return >> e-mail. University Medical Center Utrecht is a legal person by public law >> and is registered at the Chamber of Commerce for Midden-Nederland under no. >> 30244197. * >> >> *Please consider the environment before printing this e-mail. * >> > > > > -- > Han ZHANG > http://publicationslist.org/han_zhang > Center for Cognition and Brain Disorder, Hangzhou Normal University > Addr: 7th Bldg, Affil Hosp of Hangzhou Normal Univ, Wenzhou Rd 126#, > Hangzhou 310015 > Fax/Tel: +86-0571-88285651 > Mobile 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) > -------------------------------------------------- > > -- Han ZHANG http://publicationslist.org/han_zhang Center for Cognition and Brain Disorder, Hangzhou Normal University Addr: 7th Bldg, Affil Hosp of Hangzhou Normal Univ, Wenzhou Rd 126#, Hangzhou 310015 Fax/Tel: +86-0571-88285651 Mobile Tel: 15869174768