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Dear FreeSurfer experts,
I am reading your work 'False positive rates in surface-based anatomical analysis' and having several questions about multiple test correction in mri_glmfit-sim:
1. The permutation is permuting the design matrix, but how to permute it in a one-sample t-test? According to my understanding, all the subjects are listed as one group in the design matrix.
2. What's the difference between clustering-forming thresholds (CFT) and cluster-wise p value (CWP)? Whether the clustering-forming thresholds is set to the p map from the permutation test? Then how the CWP is calculated?
3. In the paper ''False positive rates in surface-based anatomical analysis, you suggested ''For surface area, one would need CFT 0.001 and FWHM>10 mm". Whether I could understand this as "the bigger smooth kernel the better"? The default smooth kernel in FSFAST is 5mm, which one should I use?
4. For the quality assurance in 'tkregister-sess', if I can use the QA value as a exclude criteria during analysis? If so is there any reference I can cite?
Looking forward to your kind suggestions.
Best regards,
Lizhi