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]
> <mailto:[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.
