Dear Stephen, list,
good to see that we largely agree on this when it comes to practicalities. Still, when answering the question 'does SPM show/store data in neurological/radiological convention' (which was what I did), there is no easy answer as in reality 3D handedness is what it is all about. Users must grasp such a concept before they can decide what they are really looking at or need to fix when dealing with 3D coordinate systems.
Therefore I'd like to propose we refrain from using the concepts neurological or radiological convention altogether, as they simply don't apply anymore in current software packages dealing with 3D/4D data.
Cheers,
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: Fromm, Stephen (NIH/NIMH) [C] [[log in to unmask]]
Sent: Sunday, March 18, 2012 1:33 PM
To: Neggers, S.F.W.; [log in to unmask]
Subject: RE: images in spm99 and spm8
Yes, but handedness is not intrinsic to image files, since the data are physically arranged in a linear (1-D) fashion; it's only given meaning by the programs that interpret the image files. If there were no software bugs and if all software (on scanners and on analysis platforms) adhered to the same standards, there'd never be an issue. Unfortunately, that's not the case.
When there's a question about the validity of a claimed handedness, the easiest way to check is an orthoview (in SPM-speak). For most brain images, it's extremely easy to distinguish S from I and A from P, but it's not so easy to distinguish L from R. To complete a handedness check, one typically does handedness-preserving rotations (i.e., no flips) until the image A,P,S,I agree with the display conventions, and then tries to make a judgement on L and R (based on vitamin E capsules, etc). At that point one can conclude that the handedness assumed by the software is correct or incorrect. But the common naive step here is something like "left is on right, but the software thinks left is on left."
I agree that it's wrong to think "the data are stored in [radiological | neurological] convention," but the notions are still useful in the limited context I outline above.
Best,
Stephen J. Fromm, PhD
Contractor, NIMH/MAP
(301) 451--9265
________________________________________
From: Neggers, S.F.W. [[log in to unmask]]
Sent: Saturday, March 17, 2012 12:00 PM
To: Fromm, Stephen (NIH/NIMH) [C]; [log in to unmask]
Subject: RE: images in spm99 and spm8
Dear Stephen,
yes of course, it *can* boil down to that when you happen to look at an axial slice, from above that is. But what when you view an image in a saggital projection, for example? Would radiological convention then mean 'up=down'?
The handedness definition is a complete definition that spans 3D space, and is as such preferable above an obsolete and underspecified definition.
And when speaking of practice: image formats nowadays (lets say the last 20 yrs) are 3D or 4D. And the way handedness is solved in nii data and SPM/FSL/AFNI is through handedness, not by flipping 2D images. When you need to check or change things to your data that have to do with handedness (or flipping, for that matter), this is the definition to check or fix. So I'd even argue that in practice, handedness makes much more sense than the obsolete radiological or neurological convention.
Just my 2 cts...
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]
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
--------------------------------------------------
________________________________________
From: Stephen J. Fromm [[log in to unmask]]
Sent: Saturday, March 17, 2012 4:36 PM
To: [log in to unmask]; Neggers, S.F.W.
Subject: Re: images in spm99 and spm8
"There is no such thing as radiological or neurological convention for 3D images. Those are concepts from a time people believed brains were flat.
"One speaks of left-or right handed image handedness in 3D, as that fully defines the coordinate systems that are used."
I agree, but I would assume radiological/neurological is still useful, as a practical description, for deciding whether there's a handedness compatibility problem. (E.g. "should be left-on-left, is displayed as left-on-right".)
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