Dear Raj,
As John pointed out before, formally nifti nor any other 3D format
represents L-R, L-R is a thing from the 2D (slice based) past. Nifti
represents only the handedness of a coordinate system, it can as well be
a mirroring of LR, up-down, or front-back. That is really what it does,
left-right is only one way the choice of a left- or right handed
coordinate system can manifest itself. The only correct way of
discussing 3D coordinate system in this context is to talk of a right or
left handed coordinate system.
In SPM5 one can see whether one deals with a left-handed or right handed
coordinate system by inspecting the voxel size (and especially the -
before the x) to see whether one deals with a left handed or right
handed coordinate system.
See http://nifti.nimh.nih.gov/nifti-1/ for details.
It of course is also relevant to understand how your raw scanner data
gets converted into nifti, there is no guarantee that the program you
use for that does this correctly (there are many). The best way to check
that would to scan a few subjects with a marker on their left or right
forehead.
Good luck,
Bas
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Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
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-----Oorspronkelijk bericht-----
Van: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
Namens Rajeev Raizada
Verzonden: donderdag 6 november 2008 0:12
Aan: [log in to unmask]
Onderwerp: [SPM] Q: Command to tell whether a Nifti image actually
contains L-R info within it?
Dear SPM list,
I had been under the impression that Nifti files always have L-R info
built-in to them, so that you never need to worry about
interpretation-conventions etc.
However, it seems that although Nifti images possess the *capability* of
having built-in L-R info, they don't have to use it.
An image can be in Nifti format without actually having that info
built-in.
If I open such an image in FSLview, it opens it and views it fine, but
it says "Coordinate space: unknown", and does not show any L-R / A-P
labels on the image view.
Is there a Matlab or SPM command which can tell me whether a particular
Nifti file has L-R info built-in to it?
I had thought that maybe spm_get_space would do that, but that command
gives a matrix of output without complaining, even when I give it a
"Coordinate space: unknown" image as input.
I've looked around a bit online, but the only discussions I can find
about how L-R info gets built-in to Nifti images are epic poems about
RAS, LAS, world-spaces and quaternions.
Any simpler or more digestible answers would be greatly appreciated!
Many thanks,
Raj
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