Hi all,
Our Siemens scanner has recently undergone a software upgrade. Now the
images we get raw from the scanner are unaveraged mosaics: 52 "super-slices"
for a 12 direction + 1 b0 scan. They used to be averaged non-mosaic volumes.
With each of the new mosaic datasets processed with FSL, I am having the
same problem: The V1 vector field looks very strange. I tried to attach
screen grabs from fslview, but the email became too big for the list.
Anyway, in axial slices, the eigenvector field is asymmetric, so the corpus
callosum is half red and half green. The
CSTs in the coronal slice are a more washed-out blue than they should be.
Clearly this is not a matter of flipping eigenvector components, and there
is no possibility of any reasonable tractography in this data.
I am at a loss as to why it should be like this. The strange thing is that
it has only happened since the software upgrade, with the unaveraged mosaic
format scans - I got good results from the old format. I am reasonably
confident about my mosaic averaging method.
Any suggestions will be much appreciated.
Regards,
Peter
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