I am confused as to how SPM99 treats the orientation of CTI7 files. Our PET
files are acquired in radiological orientation (L is R) and upside down
(Superior is -Z) relative to SPM/Analyze conventions. I have the spatial
normalization defaults for the affine transformation set to
sptl_Ornt = [0 0 0 0 0 0 -1 1 1 0 0 0]; % Radiological Convention (L is R)
I've noted two odd things. First the spatially normalized files have the
correct SPM superior-inferior orientation (Superior = -Z) even though the
affine
transformation does not specify a superior/inferior flip.
Second, even though the spatially normalized images have left side = - X,
the
left/right orientation is incorrect, i.e., the right side is labeled as
left.
Does SPM99 somehow read the orientation of CTI7 PET files from the image
header
and then automatically perform the proper flips to bring the spatially
normalized images into SPM/Analyze/Radiological orientation ? Is this
specified
when the *.mat files are written as part of the realignment routine ? If so,
should the default for the affine transformation of CTI7 files be set to no
flips, i.e.. Neurological Convention (R is R)?
sptl_Ornt = [0 0 0 0 0 0 1 1 1 0 0 0]; % Neurological Convention (R is R)
Thanks
sg
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====================================
Steven Grant, Ph.D.
Cognitive Neuroscience of Addiction Program
Clinical Neurobiology Unit
Div. Treatment Research & Development
National Institute on Drug Abuse
Room 4-4238
6001 Executive Blvd
Bethesda, MD 20892
301 443-4877 (voice) 443-6814 (fax)
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