Thanks for looking at my mail and sorry for the late reply. To remind everyone, the issue I raised is about re-orientation with mri_convert where width, height and depth are different.
On Dec 16, 2007, at 10:27 PM, Doug Greve wrote:
did you look at the help for mri_convert concerning the orientation?
I did. Let me try to better re-phrase the problem as I see it.
I wrote a ruby script (attached for fun) to generate a 90x30x10, 8- bit, equal spaced mgh file with all 27,000 voxels set to 255 and the direction cosines set to LIA orientation.
Next, I did
mri_convert --out_orientation PIL test_lia.mgh test_pil.mgh
and examined the output voxels.
The breakdown is:
24,000 voxels are set to zero. 3,000 voxels are set to 255.
The spacial pattern is sort of random looking although I am sure it is related to how it is sampling off-volume.
Is this the expected behavior?
By contrast, if you create a 30x30x30 volume of all 255, the PIL reoriented volume is identical--30x30x30 all 255. Which is completely what I would expect.
Best regards, Ray