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Topic: Masking and the cluster threshold estimator

adam_mclean
Junior Member

posted 28 August 2007 00:07

I've been running the cluster threshold estimator (CTE) on some of my data sets in combination with masks and I've been surprised about some of the results. For a particular contrast I created two VMPs, one that masked out the activation outside of the brain (VMP #1) and one that didn't (VMP #2). Out of curiosity I ran the CTE on both of these VMPs. I used the estimated smoothness that BV calculated and in both cases I used the same mask I used on VMP #1 to eliminate the activation outside of the brain. As I understand it, the CTE plugin only uses this mask to create smaller random maps and in no way applies it to the real VMP. After 1000 iterations I got two different answers for the minimum cluster size for my two VMPs. For VMP #1 (the one with the mask applied first) the minimum cluster size was larger than VMP#2. At first this seemed a bit backwards, why if I had eliminated noise outside of the brain did the minimum cluster size increase? I've come to the conclusion that in applying the mask to the VMP (VMP#1) first and eliminating the smaller noisy clusters outside of the brain, the effective smoothness of the VMP was increased. Because this smoothness is applied to the random maps to simulate spatial correlation, the random maps created for VMP#1 end up being larger on average than those for VMP#2. So, everything makes sense, but the big question now is which method is better? Is it better to make estimates on the spatial correlation of voxels just in the brain (i.e. apply the mask before the CTE) or over the entire field of view?

Fabri
Moderator

posted 03 September 2007 08:12

In order to avoid ambiguity between simulation and thresholding it is advised to use right the same mask for map estimation/generation and map thresholding.

For instance, if you run a GLM, you should specify the mask BEFORE running this GLM (you can do that in the options of both the SS and the MS-GLM dialog, upon specification of the design matrix).

If you use a different mask for GLM (or don't use a mask at all) and then you specify a mask "post-hoc" for "restricting" simulations you get the result that:
1) the mask is not effective for smoothness estimation;
2) the mask applies to simulated maps but not to the final map (the plugin is not allowed to exclude voxels outside the mask because these were not excluded from the analysis).

In conclusion, I would use the mask (or create a mask beforehands, e.g. a brain mask from the VTC or VMR (use the segmentation tool -> define VOI -> create MASK)) and use this mask for both GLM and CTE. You will see that the smoothness estimation and the final threshold will be effective within this orignial mask.

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