Hi all,
(first positing, long time lurker though).
I'm trying out the sienna scripts on some rat structural T2-weighted data and it all
works quite well (bet, flirt regs and fast output) and it generates flow maps which
agree with the very obvious reduction in grey matter volume in these brain-injured rats.
2 questions:
1. I can't find the 'make_edges' script that was alluded to by Steve in a prior post (and the
original Brain-2007 paper does not help me). I have an up-to-date install of fsl but it's not there.
Any ideas or any instructions on how best to do this?
2. Despite careful cropping of the baseline and injured data inputs to ensure similar bits of brain are present
in both, I always get the most anterior or posterior slices being labelled as 'atrophied' or 'growth enlarged' in
the A_halfwayto_B_render.nii.gz image. My template is larger than the input brains- is this a case of not using the
siena options: '-t -b' ? If so, I'm not sure how to set these for the ant-post 'Z' direction in a rat.
Thanks for any help, and BTW, you do a great service to the neuroscience community by providing such great support.
cheers,
-neil
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