Hi,
I'm preparing data from a scanner (varian) for nifti format and fsl
analysis. I have the data in the nifti format, correctly labeled in qform
and sform, but it is in neurological storage order. I was hoping to use
fslswapdim to change the file into FSL's preferred axial HFS radiological
format, but on reading the fslswapdim and fslorient notes am not sure what
they'll do.
A point to note here is that the data, while inconveniently ordered, is
correctly labeled. So I need to swap the handedness of the data and the
header information together, since they match.
I get the following information from the FSL documentation:
1. fslswapdim will reorder the data and header together UNLESS the requested
action will change the handedness of the data (my case), in which case the
"data will be swapped but the header will not". (this seems to dash my hopes).
2. Other suggestions include using fslswapdim -x y z and fslorient
-swaporient; however my data (prepared for all scan orientation in this
neurologically ordered scanner) wouldn't be handled by -x y z in all cases,
and the documentation for fslorient -swaporient states only that it "swaps
FSL radio and FSL neuro" and I'm not sure what that means or what it will do
to a general header.
So, can the fslswapdim program be made to modify the data as I want,
changing the data and the header consistently from neuro to radio while
preserving their correspondence?
Mike Rohan
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