Hello VBM experts and non-experts (like me),
I am in the process of running a VBM analysis, comparing young vs. older adults, and I am interested in how grey matter intensity relates to a number of covariates of interest differentially in these two groups.
The issue I am having is that when I run the TFCE procedure, very little/nothing remains significant, despite having t-values that are > 4 (and the pattern of results makes a lot of sense in terms of my hypotheses). There are however, many small clusters, but several larger clusters above t=3.5, for example. There are 13 subjects in one group and 15 in the other, so I suspect that I have enough statistical power for this analysis.
Here's the parameters entered into the randomise command using TFCE:
randomise -i GM_mod_merg_s3 -o GM_mod_merg_s3 -m GM_mask -d design.mat -t design.con -n 1000 -T -V
I used 1000 permutations for this preliminary look at the data to save time (rather than 5000 or 10000 permutations for the finalized, "proper" analysis).
Since the t-maps make sense, and the t-values are high, rather than using the TFCE option, I was thinking of:
1) generating the t-maps using the voxel-based thresholding method (option -x):
randomise -i GM_mod_merg_s3 -o GM_mod_merg_s3 -m GM_mask -d design.mat -t design.con -x
2) then defining the clusters at a particular threshold (taken more-or-less from the FSLwiki guide, in this example t-threshold = 4):
cluster -i GM_mod_merg_s3_tstat1.nii.gz -t 4 -o cluster_index --osize=cluster_size > cluster_info.txt
3) then using fslmaths to extract a binary mask of the clusters of interest (taken more or less from the FSLwiki guide, in this example, cluster ID #1):
fslmaths -dt int cluster_index -thr 1 -uthr 1 -bin cluster_mask1
So my questions are:
1) Is this appropriate?
2) How do I determine what t-threshold to use (in step 2, above)?
3) Am I missing something, or is anything ill-advised?
4) Is there a better way?
There was a similar post dating back to 2009, but I could not find a message with a solution to this problem.
Thanks!
Stuart
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Stuart Fogel | PhD
Research Scientist
Brain & Mind Institute | Department of Psychology
Western University | London | Ontario | Canada
www.BMIsleeplab.uwo.ca
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