Dear Mark,
I did TBSS analysis for two groups of children 5- 15 year old and I registered in TBSS_2 to a template designed for that reason then I ran Randomise command line and every thing was ok.
I used atlasquery -a "JHU white-matter tractography atlas" - m mean_FA_skeleton_mask and I got the probability value for every tract.
In order to calculate the mean FA on the skeleton for every subject I used the following command line:
fslmeants -i all_FA_skeletonised -m mean_FA_skeleton_mask
Now I want to calculate the mean FA value for every tract, I did the following as in WIKI:
cluster -i myinputimage -t 2.5 -o cluster_index --osize=cluster_size > cluster_info.txt
Then I extracted the cluster 7 using :
fslmaths -dt int cluster_index -thr 7 -uthr 7 -bin cluster_mask7
as a mask in the following command line
fslmeants -i all_FA_skeletonised -m cluster_mask7
Is this right or I am missing something? also is it correct to use JHU atlas for this analysis i.e my groups are between 5-15 year old and the mean age in JUH atlas is 29 y/o
Thanks a lot
Mohamad
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