| T O P I C R E V I E W |
| ch186 |
Posted - Sep 04 2013 : 1:34:55 PM
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).
Thanks! |
| 3 L A T E S T R E P L I E S (Newest First) |
| syam.gadde |
Posted - Sep 04 2013 : 2:23:27 PM
In that case, you could use:
fslorient -getsform IMAGE.nii.gz
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. |
| ch186 |
Posted - Sep 04 2013 : 1:58:11 PM
I just emailed you a link to the data. The S/I labels are actually incorrect (not just viewing upside down). |
| syam.gadde |
Posted - Sep 04 2013 : 1:41:57 PM
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... |
