First, it's only for Analyze. Nifti is handed-ness aware.
Second, the way it works is that the "flip" is for the entire analysis path. I'm pretty sure that's for all SPMs after but not including SPM99. (You can search the archives for further elaboration, particularly posts by John Ashburner.)
Since L/R is pretty tricky due to the high degree of L/R symmetry in the brain, it's always nice to confirm what's going on with a representative subject. (One with either a vitamin E capsule on one noted side of the brain, or one whose head was tilted L or R going into the scanner, wtih a corresponding lab notation made.)
Best,
Stephen J. Fromm, PhD
Contractor, NIMH/MAP
(301) 451--9265
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From: Modestino, Edward J *HS [[log in to unmask]]
Sent: Saturday, May 15, 2010 11:47 AM
To: Fromm, Stephen (NIH/NIMH) [C]; [log in to unmask]
Subject: RE: Radiological to Neurological convention
So, you are saying that SPM8 automatically flips images? I will check the *.m file setting.
________________________________________
From: Stephen J. Fromm [[log in to unmask]]
Sent: Friday, May 14, 2010 8:42 PM
To: [log in to unmask]; Modestino, Edward J *HS
Subject: Re: Radiological to Neurological convention
If I recall correctly, it was never necessary in SPM to flip the images (outside of SPM) before using SPM.
The main change in orientation (really, "handedness") came in SPM2, if I recall correctly. In SPM99 and before, SPM would flip the images from radiological to neurological orientation at the warping step (if necessary---i.e., if the images started out radiological). In SPM2 and after, that's no longer true.
SPM8: What you do is set the "switch" in your SPM8 installation. I think it's the file
spm_flip_analyze_images.m
If your analyze images are radiological, you'd set
flip=1
If neurological
flip=0
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