Dear FSL experts,

I am still trying to understand whether the tbss_tfce_p_tstat output  
from TFCE is returning uncorrected p-values that are specific to each  
cluster that is found in a tract?  I am assuming this because some  
voxels have a higher uncorrected t-value but yet a higher uncorrected  
p-value than other voxels located in other tracts.  So each found  
cluster follows its own t-distribution with its own degrees of freedom?

Also, does thresholding the tbss_tcfe_corrp_tstat to 1-P=.95 give the  
clusters in tracts that survive a "p<.05 threshold, corrected for  
multiple-comparisons?"

Finally, with a sample size of N=22 (11 in clinical group, 11  
controls), I found several clusters in tracts that survive at the  
uncorrected 1-P=.95 level for tcfe_p_tstat, but no clusters in tracts  
that survive at the corrected 1-P=.95 level for tcfe_corrp_tstat.  Is  
this simply a power issue?  I added more subjects to obtain N=34 (21  
clinical, 13 controls), but I still only find tracts that survive at  
corrected 1-P=0.8 level (but none at .95) for the tcfe_corrp_tstat.

Thank you for your time,
Mark Shen
M.I.N.D. Institute
University of California, Davis


On Nov 19, 2009, at 9:52 AM, Michael Harms wrote:

Re (1): Yes, it is the raw t-value, and will be the same as if you used
if the -x (voxelwise) and -c (cluster) options.  In fact, if you use all
options simultaneously, you get just a single <root>_tstat1.nii.gz file.

Re (2): Yes, <root>_tfce_p_tstat is the map of uncorrected p-values for
the TFCE statistic (although I'm not sure how that is calculated given
that the TFCE doesn't have a parametric distribution).

Re (3): Yes, <root>_tfce_corrp_tstat is the FWE corrected p-value.
According to the Smith and Nichols (2009) paper on TFCE, it is based on
the maximum (voxel-wise) TFCE value (across permutations).  Thresholding
at 0.95 to 1 will give you VOXELS (which may or may not be contiguous to
other voxels within that range) that survive the voxel-wise FWE test of
the TFCE value.

cheers,
Mike H.

On Thu, 2009-11-19 at 17:23 +0000, Mark Shen wrote:
> I followed the TBSS v1.2 manual, and after creating .mat & .con  
> files for a
> two-sample unpaired t test, I ran the following randomise script  
> for TFCE:
>
> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d
> design.mat -t design.con -n 500 --T2 -V
>
> Outputs generated:
> tbss_tstat1
> tbss_tstat2
> tbss_tfce_p_tstat1
> tbss_tfce_p_tstat2
> tbss_tfce_corrp_tstat1
> tbss_tfce_corrp_tstat2
>
> Questions:
>
> (1) Is tbss_tstat the raw, uncorrected t values?  If it is raw and
> uncorrected, should this t statistical map be identical to the  
> tstat outputs
> from using voxel-wise or cluster-based thresholding options?
>
> (2) Is tbss_tfce_p_tstat the uncorrected p values?  Am I right to  
> say that
> this is not corrected for FWE multiple comparisons, but TFCE is  
> returning
> uncorrected p-values that are specific to each cluster that is  
> found?  (I am
> assuming this because some voxels have a higher uncorrected t-value  
> but also
> higher uncorrected p-value than other voxels located in other  
> tracts.  So
> each found cluster follows its own t-distribution?)
>
> (3) Is tbss_tcfe_corrp_tstat the FWE corrected p values?  Thus,  
> thesholding
> this to .95-1 gives the clusters that survive a "p<.05 threshold,  
> corrected
> for multiple-comparisons?
>
> I found several clusters that at 1-P=.95 level for tcfe_p_tstat,  
> but no
> clusters that survive at the 1-P=.95 level for tcfe_corrp_tstat.   
> Is this
> simply a power issue?  This analysis has N=22 (11 in clinical  
> group, 11
> controls), but I am adding subjects to obtain N=34 (21 clinical, 13
> controls) and will ultimately have N=100 (70, 30).
>
> Thank you!
>
> Mark Shen
> UC Davis M.I.N.D. Institute