Hi - this all sounds fine, assuming your design.mat and design.con are  
correct.   You also might like to load all_RD_skeletonised into  
FSLView and turn on "timeseries" and check that you have valid,  
varying, data on the skeleton. Sounds like you probably do.

The beauty of TFCE is that it is designed to be sensitive to both  
focal, strong, effects, as well as diffuse, less strong effects - so  
it seems like possibly you have a very diffuse (i.e. covering lots of  
the skeleton), low effect that correlates with your model.   There is  
nothing invalid about thism as randomise is still valid for this  
scenario. You might want to show both the p<.05 corrected map (lots of  
voxels surviving) and also a more conservatve thresholding (e.g. p<. 
005 etc) for also showing where the effects are stronger.

Cheers.



On 30 Mar 2009, at 20:00, Yi-Shin Sheu wrote:

> Dear FSL experts,
>
> I am looking at a set of DTI images in terms of FA, MD, L1 and RD  
> (L2+L3)/2
> images.
>
> I didn't get any significant TBSS result for FA, MD, L1, however,  
> when I ran
> TBSS on RD images, I got a corrected p of 0.002 for the same contrast
> (patient > control) and same design matrix.  When I check the tfce  
> correct p
> stats, and threshold them at p<0.05 (in fslview, I put down 0.95),  
> it is pretty
> much the "entire" RD skeleton was significant, which is really  
> awkward.
>
> I went back and visually check the raw RD images, normalized RD  
> images, and
> RD skeleton, everything was normal.  However, I still feel something  
> is wrong,
> so here is my tbss_non_FA pipeline.
>
> 1. copy the L2 images and L3 images for each subject, and use  
> fslmaths to
> derive the average of these two.
> 2. creat a RD folder contaims all the Rd images, and make sure the  
> naming is
> the same as images in "origdata"
> 3. Run tbss_non_FA RD
> 4. Run randomise -i all_RD_skeletonmised -o tbss_RD -m
> mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V
>
> Did I miss any step?  I read some of the FSL threads that I might  
> need to
> scale the RD images.  By the way, the intensity in my RD skeleton  
> image
> ranges from 0 to 0.001.
>
> Kindly advise.
>
> Yi-Shin
>


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