Roddy McColl wrote:
>...
> with orientation of the data. My processing pipeline is
> DICOM -> to3d -> AFNI -> 3dAFNItoNIFTI -> eddy_correct -> TBSS
> however I find that in fslview (latest - 2.4.0b) the labels
> are wrong (L-R instead of R-L and axial slice is upside down
> even though labeled correctly i.e. P is up, A is down).
Hi Roddy,
Do you mean that the hemisphere labelled left should be labelled right
(e.g. from confidence in DICOM viewer or oil-capsule or something) or
are you just concerned that the image is not shown with left on the
left/right side of the screen as you expect? (it sounds like this is
the case with A-P).
The actual layout of the display shouldn't matter at all as long as
the labels are anatomically correct. So don't worry about the A-P
up/down thing as long as A is anatomically anterior.
If left and right are labelled opposite to anatomy, then I think you
just want:
avwswapdim -x y z
(and certainly just one flip, if the A-P & S-I labels are correct)
Hope that helps,
Ged.
>...
> Original data are true axials.
> avworient -getorient returns NEUROLOGICAL.
> I am not trying to finger point wrt AFNI vs FSL vs NIFTI,
> but I suspect that I will not be able to push my data through
> TBSS until the orientation issue is worked out.
> I have tried
> avworient -forceradiological
> and
> avwswapdim x -y z
> and
> avswapdim -x y -z
> and none (individually) has solved the problem in the sense
> that fslview on the result doesn't produce what I expect which
> is Coronal with S-I and R-L, Sagittal with S-I and A-P and
> Axial with A-P and R-L.
> Any suggestions gleefully received.
> -r
>
> Roddy McColl
> UT Southwestern
>
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