What is the easiest way to flip the orientation labels on a functional image? After reconstruction, our data from the 32-channel head coil has the S/I Labels backwards. Is there a simple way for me to fix this now that I have the .nii file? I tried just loading it into MATLAB and using flipdim but couldn't get that to work with the 4D data (which I might have been doing it wrong).
Do you mean the S/I labels are not correct with respect to the brain, or that the labels are correct and superior and inferior are just displaying upside-down compared to how other images are displayed?
If the former, it needs to be fixed.
If the latter, there are some solutions.
Could you send me a pointer to the data privately and I'll take a look...
This gives you a list of 16 numbers which correspond to the matrix:
X Y Z trans R 1 2 3 4 A 5 6 7 8 S 9 10 11 12 [0] [0] [0] [1]
Negate the numbers occuring in whichever column corresponds to the S/I axis (i.e. if it's the slice axis, negate the third (Z) column.
Then put those numbers back:
fslorient -setsform [16 new numbers...] IMAGE.nii.gz
Do the same for -getqform/-setqform .
Maybe there's a better way, but most tools start with the assumption that the input orientation labels are correct. If this is a one-off, it's not too bad.
Flipping orientation labels
Posted - Sep 04 2013 : 1:34:55 PM
