Hi Parisa, cc all,
are you referring to voxel space or mm space? In mm space the origin is always at 0,0,0 and never anywhere else, by definition. It is of course possible that the origin in one coordinate system (say mm space) is at a non-zero location in another coordinate system (say voxel space). When having a formal geometrical discussion about a concept as 'origin', this is impossible without specifying what coordinate system you are using or referring to.
So I still don't fully get what your problem is, but I do have a hunch.
In practice, the origin of the mm-coordinate system of your image expressed in voxel space is 100% independent of the viewer you use, as it implicitely encoded in the voxel-to-world mapping in the nifti format header (see the formal nifti specs at http://nifti.nimh.nih.gov/nifti-1/). As long as the nifti viewer you use is fully nifti-aware they will show up the same. Mricron and SPM both are fully nifti aware. When you really use the older Mricro, that wasn't fully nifti aware the last time I looked at it (couple of years ago). When you want geometrical correspondance between images you look at in a viewer, I strongly suggest using mricron and SPM, and ditching Mricro.
Good luck,
Bas
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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.brainsciencetools.com (CEO)
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________________________________________
From: parisa Tahafchi [[log in to unmask]]
Sent: Wednesday, October 03, 2012 11:58 PM
To: Neggers, S.F.W.
Subject: Re: [SPM] Change Origin
Hello Bas,
Thanks for your swift response. My CT(source Image) and MRI(target) images have [0,0,0] origin in MRIcro. When I register them with SPM(coregistration), The origin of result image is [12.5,140.5,111.5] in MRIcro.
The dimensions of CT and MRI images are [332,352,216],[240,280,222] respectively.
Many thanks in advance,
Parisa
________________________________
From: "Neggers, S.F.W." <[log in to unmask]>
To: [log in to unmask]
Sent: Wednesday, October 3, 2012 2:57 PM
Subject: Re: [SPM] Change Origin
Could you be more specific? 0,0,0 is always the origin, by definition...
Cheers,
Bas
--------------------------------------------------
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]><mailto:[log in to unmask]<mailto:[log in to unmask]>>
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
--------------------------------------------------
________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]<mailto:[log in to unmask]>] on behalf of parisa Tahafchi [[log in to unmask]<mailto:[log in to unmask]>]
Sent: Wednesday, October 03, 2012 12:40 PM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: [SPM] Change Origin
Dear all,
I did a coregistration with SPM for MRI and CT images with [0 0 0] as origin.
But my result has a different origin when I see them in MRIcro,
I appreciate it if anyone could give a explanation about how I can change this origin to something else or zero for example.
should I do this manually in MRIcro?
Many thanks in advance,
Parisa
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