Hi Han,
you are right, what Bas calculates is not the voxelsize but the position
of the corner of one voxel. It is the voxel position 1 1 1 transformed
to mm space ( by the way inv(mat)\[1 1 1 0]' is the same as mat*[1 1 1 0]').
you can also use:
voxelsize=sqrt(sum(mat.^2))
Michael
Am 25.11.2011 14:00, schrieb han zhang:
> 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]
> <mailto:[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]
>> <mailto:[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]
>>> <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] <mailto:[log in to unmask]>
>> Web :http://www.neuromri.nl/people/bas-neggers
>> :http://www.neuralnavigator.com <http://www.neuralnavigator.com/> (CEO)
>> --------------------------------------------------
>>
>> ------------------------------------------------------------------------
>>
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>>
>>
>> --
>> 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] <mailto:[log in to unmask]>
> Web :http://www.neuromri.nl/people/bas-neggers
> :http://www.neuralnavigator.com <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
>
--
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Dr. Michael Erb
Dep. Neuroimaging and MR-Physics
University Hospital Tübingen
Hoppe-Seyler-Str. 3
72076 Tübingen, Germany
Tel.: +49(0)7071/2987753 priv. +49(0)7071/61559
Fax.: +49(0)7071/294371
e-mail: <[log in to unmask]>
www: http://www.medizin.uni-tuebingen.de/nrad/sektion/
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