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Hi Chen-Chia, Please see below: On Sat, 20 Oct 2018 at 06:06, Chen-Chia Lan <[log in to unmask]> wrote: > Dear FSL experts, > > I have a question regarding using prethreshold maksing with randomise and > TFCE options in FEAT GUI. > I tried to do a group analysis with randomise with 5000 permutations with > TFCE, without and with a bilateral nucleus accumbens mask. > > I understand that by using the prethreshold masking, the null-distribution > for FWE correction will be different from that without this prethreshold > masking, so a voxel's FWE corrected p-value will change depending on > maksing or not. > > What about the TFCE value itself for a voxel in the mask? > It changes too, because TFCE depends on "other" voxels, some potentially being outside the mask. TFCE isn't a pivotal statistic. > Does the pre-threshold maksing change the "cluster support" for a voxel's > TFCE value? > It may change (invariably it does) the support region, yes. > What I mean is when using prethreshold masking with TFCE, does a voxel > from outside the mask still contribute to the TFCE value for a voxel within > a mask? > No, the pre-threshold masking puts these external voxels away. > Or should the TFCE value of a voxel within the mask only be contributed by > other voxels within the mask? > Correct. > I am assuming the former is the case, as the masking is "prethreshold", so > the voxel statistics would be calculated in the same way before the masking > anyway. > It's the latter. > And I think this is why the thresh_pstat*.nii.gz I get from with and > without masking are exactly the same because they are uncorrected p-values? > > Your results show clusters of same size but different p-values. In one case the z-stat is the same, and it may have been a coincidence (just 2 decimal places), since the voxels are different. All the best, Anderson > > The result of one particular contrast showed without masking is as > followed: > > Cluster Index Voxels P -log10(P) Z-MAX Z-MAX X (mm) > Z-MAX Y (mm) Z-MAX Z (mm) Z-COG X (mm) Z-COG Y (mm) Z-COG Z > (mm) COPE-MAX COPE-MAX X (mm) COPE-MAX Y (mm) COPE-MAX Z (mm) > COPE-MEAN > 9 45409 0.0142 1.85 3.54 8 -28 -36 -1.68 > -26.5 12.8 59.2 2 -38 2 16.1 > 8 153 0.0378 1.42 3.24 -24 -52 44 -27.3 > -52.4 47.6 23.9 -32 -56 52 13.5 > 7 148 0.0388 1.41 3.24 20 42 -14 22.1 > 47.5 -13.9 12.5 30 46 -16 8.44 > 6 79 0.0438 1.36 3.35 50 -18 -26 46.9 > -16 -24 12.2 44 -16 -24 9.1 > 5 50 0.0468 1.33 2.54 42 -52 -12 46.1 > -51.3 -14.3 14.5 44 -52 -14 12.9 > 4 26 0.0462 1.34 2.79 -24 56 -12 -24.5 > 56.9 -11.4 10.5 -24 60 -10 8.8 > 3 19 0.049 1.31 2.44 44 -10 -16 41.3 > -9.07 -14.3 15.2 42 -10 -14 13.2 > 2 11 0.0492 1.31 2.58 -24 -46 -6 -24 > -46.9 -6.17 16.3 -24 -48 -8 13.2 > 1 4 0.0494 1.31 2.45 -26 -64 -6 -26.5 > -64.5 -6.5 11.9 -26 -64 -8 11.4 > > > The result with the same contrast with maksing is as followed: > > Cluster Index Voxels P -log10(P) Z-MAX Z-MAX X (mm) > Z-MAX Y (mm) Z-MAX Z (mm) Z-COG X (mm) Z-COG Y (mm) Z-COG Z > (mm) COPE-MAX COPE-MAX X (mm) COPE-MAX Y (mm) COPE-MAX Z (mm) > COPE-MEAN > 2 45409 0.0026 2.59 3.54 -14 10 -10 -0.212 > 12.6 -4.7 59.2 2 -38 2 16.1 > 1 153 0.047 1.33 0 -24 -54 40 nan > nan nan 23.9 -32 -56 52 13.5 > > > Obviously, cluster 9 and 8 without masking correspond to cluster 2 and 1 > with masking. > From the result, I can see that with the same Zmax value of 3.54 (although > in different voxel coordinate because of the maksing), the corresponding > p-value has changed presumably due to a different null-distribution for FWE > related to the masking. > But if the previous is the case, that the null-distribution has changed, > then I don't understand why the voxels in cluster 9 without masking and > cluster 2 with masking are still the same at 45409? > Especially, in the first place, why does the result with masking still > showed a cluster with 45409 voxels which is by itself much larger than the > accumbens mask? > Why does voxels outside the mask still being formed into the cluster in > the report? > > Thank you very much! > > Best wishes, > Chen-chia > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1