For images prior to the NIFTI format, there is nothing in the header
that denotes the orientations of the images. If you want to be able to
import your registered SPM2 images into some other package, but have
them in the alignment that SPM assumes, then you'll need to reslice the
images. There is a function that can be used to do this available from:
http://www.sph.umich.edu/~nichols/JohnsGems.html#Gem7
A version for SPM5 is available in:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&P=R285835
Best regards,
-John
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Jeff Browndyke, Ph.D.
Sent: Saturday, April 07, 2007 7:49 PM
To: [log in to unmask]
Subject: [SPM] SPM2 Display Reorient. Way to write change to .hdr, not
.mat?
The inability to call up SPM2 Reoriented Images in the .mat changed
orientation in other programs (SNAP) is causing problems when we are
attempting to marry manual ROI masks to the SPM2 reoriented anatomicals.
Is there a way to permanently write the .mat orientation parameters to
the
anatomical .hdr files? I would like to have the ability to call up the
same
(corrected) orientation in several different imaging platforms. We're
stuck
right now with SPM2, so any workarounds other than the typical "upgrade
to
SPM5" would be most helpful.
BTW - we were using a resize_img script, that appeared to be based upon
J.Ashburner script functions, but the resulting files were reduced in
image
intensity and appeared smoothed eventhough we did not change the voxel
sizes
(only the origin/orientation).
Thanks,
Jeff
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