Remember, the whole problem with the Analyze format is that it's not handedness-aware. In fact, it's not really orientation-aware at all.
So if we're talking about Analyze format here, then you need to set flip to 1 if the images are in radiological format, and 0 if in neurological, regardless of how the Analyze images were created. Of course, perhaps SPM's DICOM toolbox will always put them in one form or the other, and ditto for MRIcron---I'm not sure. You'd have to read the documentation. It's possible that the DICOM toolbox would check the "flip" setting before creating Analyze format images, though my best guess is that it doesn't.
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 5:56 PM
To: Fromm, Stephen (NIH/NIMH) [C]; [log in to unmask]
Subject: RE: Radiological to Neurological convention
Does SPM only flip images when you import DICOM files directly using SPM? If you convert DICOM files over with MRIcron and then open them in SPM, is this different? Will SPM not flip them then?
________________________________________
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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