Hi,
It isn't important to get the origin in the same place (or have the same
mm coordinate
values as the avg152) unless you are using it to report standard space
coordinates.
If the image has not been resampled to standard space then it is fine
just to make sure
that the increases and decreases in coordinates are the right way around.
What is a problem is that if your x millimeter coordinate is
_increasing_ if you move
_left_. It *must* decrease in order for the left-right ordering of your
image to be
correct. As it stands, the labels attached to L-R in FSLView are likely
to be the
wrong way around (which is the easiest way to see if FSL is correctly
interpreting
things or not). If this is the case, then I suggest you run avworient
-swaporient on
your data and then check it again. Hopefully that will restore the
labelling in FSLView
to the correct one. Once this labelling is correct then you can proceed
with
confidence (as long as it isn't meant to be in standard space - see above).
All the best,
Mark
Suzanna Laycock wrote:
>Hi everyone,
>
>I have a query about changing ones data into the radiological orientation.
>
>The FAQ section on the FSL website states the following:
>
>- z-axis as the inferior-superior direction (moving in the superior
>direction increases the z voxel index and the z millimetre coordinate)
>- y-axis as the posterior-anterior direction (moving in the anterior
>direction increases the y voxel index and the y millimetre coordinate)
>- x-axis as the right-left direction (moving in the left direction increases
>the x voxel index but decreases the x millimetre coordinate)
>
>The z and y axises on my FA image are correct (according to the above), but
>the x-axis doesn't seem to work. I know which is left and right, so placing
>it in the above orientation, moving left increases the voxel index, but also
>increases the x millimetre coordinate. Having looked at avg152T1_LR-marked
>, I notice that the mid-sagital slice has an x-axis millimeter coordinate of
>0.
>
>Do I need to adjust my data to have this exact same coordinate, and if so
>how do I do it? Or is it okay for the left and right of my FA image to be
>in the same orientation as avg152T1_LR-marked regardless of the millimeter
>coordinates?
>
>Regards
>Suzanna
>
>
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