Dear FSL'ers
I have been trying to use BET2 on analyze files made in SPM. I must be doing
something worng as the problem is that after extracting the brain the
orientations are wrong (i.e., different) on the extracted vs. original images.
Here is the output of fslorient for an SPM-ANALYZE file
fslorient -getsform s1094-0004-00001-000001
0.85879 0.0316479 -0.00212486 -82.5151 -0.0314743 0.85715 0.0618951 -125.362
0.00378017 -0.053088 0.99808 -60.3387 0 0 0 1
The exact same numbers are returned for fslorient -getqform
Now I run bet2.
bet2 s1094-0004-00001-000001 s1094-0004-00001-000001_brain
Although fslview can display the original and extracted images
(s1094-0004-00001-000001 and s1094-0004-00001-000001_brain) as aligned, SPM
does not. So I rechecked the orientations:
fslorient -getsform s1094-0004-00001-000001_brain
-0.859375 0 0 77.3438 0 0.859375 0 -123.75 0 0 1 -67 0 0 0 1
fslorient -getqform s1094-0004-00001-000001_brain
0.859375 0 0 0 0 0.859375 0 0 0 0 1 0 0 0 0 1
So the orientation appears to have been changed by running the image through
bet extraction.
I am running FSL within the VMware player.
Please let me know what I am doing wrong and how to avoid this.
thanks,
darren
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