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SPM  September 2007

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Subject:

Re: SVC

From:

Ged Ridgway <[log in to unmask]>

Reply-To:

Ged Ridgway <[log in to unmask]>

Date:

Tue, 11 Sep 2007 15:26:19 +0100

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Hi Doug,

> [...] the baseline is 
> determined from the mean activity and variance across all the voxels in 
> the brain [/ROI], which is then used to obtain beta values for each voxel.

I think you're referring to the estimation of the variance components, 
used with weighted least squares to estimate the betas. SPM pools all 
voxels which survive a main-effects F-test at an uncorrected 
alpha-level (set in spm_defaults.m, look for .ufp). The use of 
different explicit ("small" or otherise) ROIs would mean different 
sets of voxels would be pooled to estimate the non-sphericity, and 
hence beta could possible differ.

I guess the argument here would be similar to what Tom Nichols said 
earlier in the thread about smoothness estimation. In both cases, if a 
very small ROI is used, the estimate is likely to be very unreliable. 
On the other hand, both for non-sphericity and for smoothness, I 
wonder if one might argue that a respectably large ROI could actually 
be better than whole-brain, since both smoothness and non-sphericity 
could be non-stationary over the brain, and might be locally better 
estimated for the ROI (Tom?).

Anyway, this is probably a fairly minor point, and is slightly off the 
original question that Susie raised: does the SVC only look at voxels 
which survive the whole-brain stat thresholding that it follows? 
("follows" in the sense that you can only press the SVC button *after* 
you've specified an alpha (and optional extent threshold) for the 
whole-brain). I think it does, due to the way spm_VOI is coded (see my 
previous messages in this thread). This might not matter much, since 
if you just choose a fairly lax uncorrected threshold for the 
whole-brain, you won't be ignoring any voxels which would have any 
chance of passing a stricter and/or corrected threshold for the ROI.

I think it's an important point though, in the sense that I believe 
users expect their results after pressing SVC to be independent of the 
previous threshold they specified. So they might for example select 
FWE 0.01 as their whole-brain threshold, then (perhaps without very 
much surviving that) they might click SVC and enter their ROI, 
expecting that every voxel within the ROI will be analysed, and 
corrected for the ROI. This does not seem to be the case, for reasons 
outlined in my previous emails in this thread. Their SVC analysis in 
this case might include more if they instead clicked "results" again, 
set the whole-brain threshold to uncorrected-0.5 and then clicked SVC 
as before.

So in other words, it's predominantly an issue of 
documentation/user-expectations, that I am concerned about. UNLESS, it 
is deliberate that SVC excludes voxels that failed to pass the 
whole-brain threshold, which is seeming less likely (following 
comments from Tom and Marko), but hasn't actually been confidently 
denied by anyone. Since in this case, the use of uncorrected-0.5 above 
could be "cheating" in some way. It would be good to have this 
confirmed/denied. Possibly the usage or documentation of SVC could 
also be changed, to clarify that it won't relax a previously very 
strict whole-brain threshold.

Best,
Ged.

P.S. I have now done myself what I suggested Mahinda try: re-running 
multiple clicks of the "results" button, changing the whole-brain 
alpha, and then using SVC. It seems to me that I can indeed reduce the 
number of SVC-significant voxels (e.g. noticing changes in the K_E of 
the largest cluster) with stricter initial whole-brain alpha (SPM5, 
latest updates). Though possibly people think I am doing something 
peculiar/wrong?

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