Hi Suzanna,
> I was wondering if I could clarify measuring the
> mean FA within a ROI.
>
> I have drawn some masks in FSLview using the MN152
> and all_FA images
> as guidelines. I'm interested in the mean FA within
> those masks in
> each individual.
>
> From the list, I gathered that the following should
> do what I wanted:
> fslmeants -i all_FA -m my_mask -o output.txt
>
> The output of this was a list of values,
> corresponding to each
> participant. I presume they're the mean scaled FA
> for the ROI in a
> participant.
>
> Does this process sound okay?
Yes, it does. Don't forget to divide by 10000 the FA
values. You might also prefer to look at:
fslmeants -i all_FA_skeletonised -m
my_mask_intersected_with_skel_mask -o
output_on_skel.txt
if you looking for mean FA inside white matter tracts.
> Secondly, is there a way of determining the exact
> order of
> participants within the all_FA? Would the
> index.html in FAi/slicedir
> do this?
Yes, or a ls *_hr.nii.gz. Basically, the images are
concatenated in the alphabetical order. So, this is up
to you to put prefices so that the concatenation makes
sense with your design.mat file...
Hope this helps,
Gwenaelle
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