Hello,
Sorry to bring up orientation issues again, but I want to be 100% certain that when we view our results, right is right and left is left.
I use Freesurfer's mri_convert to convert the DICOM images (from GE 3T) to Analyze format (e.g. image001.{img,hdr,mat}, ..., imageXXX.{img,hdr,mat}). Doug Greve from NMR has assured me that mri_convert doesn't change the orientation of any of the images. It does output the .mat file containing the transformation matrix M.
Then I use SPM5 to slice-time, realign & reslice, normalise, and smooth. I have done analyses with defaults.analyse.flip = 0, and = 1. However, the results are exactly the same when I compare them. This is not true of some patients we scan, whose data we do NOT normalise, but rather co-register w/ a structural image (e.g. SPGR). The results were flipped based on the value of the default.
This got me thinking:
1) Does normalising to the template (e.g. T2.nii) automatically flip the images?
If so, when I run an analysis, will SPM even bother checking defaults.analyse.flip?
2) Does a value of 0 essentially mean "these images are in radiological convention; they need to be flipped to be viewed in neurological convention"?
3) Does the value of defaults.analyse.flip affect what I see on the screen? e.g. Will I see something different when I use the Results, Display, or Check Reg. functions if I change the value?
The reason this is so important, is that it's easy enough when we have a patient w/ a lesion to tell which side is which. But on normal subjects, even with the Vitamin E pill on their temple, it doesn't show up on the functional images. So it's nearly impossible to tell. We also have DTI data, that I manually flipped, so that using SPM's Display function, right is right and left is left. However, the FA differences and functional differences appear to be in opposite hemispheres... and I want to be sure if I'm currently doing something wrong/backwards.
Thanks to anyone that made it this far,
Chris
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