Hi groop,
I want to get into TBSS but I am continuing to have problems
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).
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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