Thanks very much for your response and the clarifications. I appreciate your
help! I have to admit that I find orientation issues extremely confusing.
Could I just attempt to further clarify things a bit?
Background: my scans were axial ANALYSE (.hdr/.img, radiological) and I
converted them to NIFTI with fslchfiletype and to coronal orientation with
fslswapdim x z y before submitting them to further processing.
So you are saying that a feature (in fact some piece of neck which remained
after removing skull) which appeared on the right part of the screen in the
axial plane before the x z y conversion, after the x z y conversion it
should appear on the left side of the screen? And to the extent that it does
not, it means that left-right flipping may have occured? So if I apply -x z
y then it would appear on the left as it should?
Would this be the recommended way of getting from the coronal to the axial
orientation in general? In case it is of help, I have attached a CT scan
image with an implanted electrode on the patients left, where the acquired
coronal was transformed to axial using avwswapdim x z y and which resulted
in the same warning message. In the resulting axial image, the electrode
still appears on the patients left. Would this mean that left-right
orientation was maintained? Would it inform at all our case?
In the case of further processing in FSL, is your recommendation not to swap
from coronal to axial, but to let FLIRT handle it by specifying the search
Thanks a million for your help -I would be lost without it!