Hi,
I have not followed the whole story, but it seems to
me that your 1_minus_grot_vox_tstat1 image is 1 in the
background *outside* the skeleton and gives you the
p-values of your analysis *inside* the skeleton...
As you want your results to be corrected among the
whole volume where you did your analysis, then the -m
mask should definitely be the mean_FA_skeleton_mask.
Also, the less conservative FDR correction accepted is
indeed -q 0.05, but this is a "default" value. If you
feel like you have (luckily) too many significant
results for this threshold, you can try with 0.01,
0.005 etc.
Hope this helps,
Gwenaelle
--- bs Jeong <[log in to unmask]> a écrit :
> Hi FSL users
>
> fdr -i 1_minus_grot_vox_tstat1 -m mask -q 0.05
>
> In fdr, which image is for the mask?
> vox_tstat1 is already in mean_FA_skeleton_mask.
> So mask in fdr would be not mena_FA_skeleton_mask.
> I think the mask would be a certain region of
> skeleton such as the area
> showed the highest significance among many tiny
> areas, rather than a
> mean_FA_skeleton_mask in TBSS and one ROI among
> several activation regions
> rather than GM mask.
>
> Does -q option have to less than '0.05'?
>
> thanks,
>
> bsjeong
>
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