I'm using spm99.
I'd like some details on how orientation is encoded in SPM, in ANALYZE
format files. For succinctness, I'll make claims, in quotations. My
question is which claims are true.
"'display' displays a template according to neurological convention: brain
left on image left."
"Regardless of its orientation (neurological or radiological), 'display'
displays an ANALYZE image which hasn't been normalized with voxels and mm
increasing from image left to image right. This is correct if the image is
in neurological/SPM-post-normalization orientation, but backwards otherwise.
In the latter case, the defaults file should be set so that "orientation" is
set to radiological."
"There is no information in the *.hdr file which allows SPM to decode the
orientation of an ANALYZE-format image that has not been put through SPM
preprocessing. If a *.img file consists of Nz slices, with the most
inferior slice first; each slice consisting of Ny lines, with the most
posterior line first; each line consisting of Nx voxels, with the rightmost
voxel first---then as far as SPM is concerned, the image adheres to the
radiological convention. If 'right' and 'left' are reversed in the previous
sentence, then to SPM the image adheres to the neurological convention. In
any event, the orientation can be discovered by displaying the image.
Subject's left appears on image left if and only if the image adheres to
neurological convention."
"In the image file, if slices (from inferior to superior) contain lines
which run from left to right, then the images will appear rotated if
displayed by SPM. Instead of reshuffling the files (so that slices contain
lines running from posterior to anterior), one can use the defaults file to
inform SPM of this; the defaults file is more flexible in specifying
orientation and allows one to specify more than just neurological vs.
radiological."
Best wishes,
Stephen Fromm
NIDCD/NIH
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