Hi,
> I believe I am trying to do a similar analysis. I
> have generated my ROI
> based on the mean FA skeleton t-test and I want to
> calculate mean FA values
> for each subject's MNI-normalized FA map. But the
> MNI-space FA maps are all
> bunched together in the all_FA.nii.gz file. Can I
> extract each subject from
> the 4D file and look at them separately?
Yes, you can use:
fslmeants -i your4D -m yourmask -o yourROIresults.txt
> Steve, you
> mentioned using the
> all_FA_skeletonised.nii.gz file (instead of
> all_FA.nii.gz). Why do you
> recommend this?
Because the FA values you've compared are the one
projected onto the skeleton...
So, if you want to be accurate, either you use your
ROI defined by your results on the skeleton and your
4D all_FA_skeletonised, or you back-project your mask
in the centre of the tracts for each individual (with
tbss_deproject) and then use each new *interpolated*
ROI deprojected and the corresponding image of the 4D
all_FA. Needless to say that the first option is
quicker and does not involve any interpolation!...
Hope this helps,
Gwenaëlle
> Many thanks,
> James
>
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