Hi Brittany,
what you want to use is tbss_non_FA. For usage, please
look at the manual:
http://www.fmrib.ox.ac.uk/fsl/tbss/index.html
in the section "Using non-FA Images in TBSS". You can
use the transformation matrices generated from the FA
registration to MD, parallel diffusivity etc.
Then yes, if you want to investigate the MD in the
*subcortical grey matter* (please bear in mind the
huge partial volume effect that may occur in the
*cortex*), you can feed directly the all_MD.nii.gz 4D
image into randomise. You might want to smooth it with
fslmaths all_MD -s 3 all_MD_smoothed (for instance)
beforehand. And you can complement the GM analysis
with the white matter study with all_MD_skeletonised
and the entire tbss processings that you've followed
for the FA.
Hope this helps,
Gwenaelle
--- Brittany Copp <[log in to unmask]> a écrit :
> Would it work to use tbss_2_reg to register the MD
> data and then run
> randomise on the registered image to include both
> white and gray matter? Or
> is there some way to apply the conversion matrices
> used when I ran the whole
> TBSS processing chain with the FA data? Thanks,
>
> Brittany
>
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