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Hi following my previous email, can I ask how to generate a
mean_MD_skeleton.nii.gz so I can use it to create a mean_MD_skeleton_mask.
My current tbss_nonfa MD output only has all_MD.nii.gz and
all_MD_skeletonised.nii.gz. However, I think to do randomise, I have to use
the same skeleton and it's mask (i.e randomise -i all_MD_skeletonised -o
tbss -m mean_MD_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V),
instead of using the mean_FA_skeleton_mask.
Is it right to do the following: I first get all the individual
MD_skeletons, then average them, and binarise the mean_MDskeleton
If my all_MD.nii.gz has 10 volumes for example

step 1:
fslroi all_MD_skeletonised.nii.gz MD_1.nii.gz 0 1
...until
fslroi all_MD_skeletonised.nii.gz MD_10.nii.gz 9 1

step 2:
fslmaths MD_1.nii.gz -add MD_2.nii.gz ....-add MD_10.nii.gz -div 10
mean_MD_skeletonised.nii.gz -odt float

step 3:
fslmaths mean_MD_skeletonised.nii.gz -bin mean_MD_skeleton_mask.nii.gz

I then use this mask to do the randomise statistics on my
all_MD_skeletonised data.

However, when I try this on the FA skeleton, the calculated mean_FA_skeleton
from this way is not identical to the one generated from tbss_4_prestats 0.2
(there's a lot less skeleton). However, to just get the mean_MD, would the
above steps be good enough?

thanks

Siewmin