External Email - Use Caution Thank you very much for your detailed explanation. About the second question, I am still confusing on the permutation and CWP map calculation:
1. Whether the CFT is applied to the uncorrected p-value map first (e.g., the sig.nii.gz generated by 'mri_glmfit')? Then we could get several clusters survived from the CFT, right? 2. But how the permutation works and generates the CWP map? I found that the CWP within a cluster is the same, but zero out clusters (perm.th30.pos.sig.cluster.nii.gz). 3. Besides, may I know what the value is in the file 'perm.th30.pos.sig.voxel.nii.gz'? Thanks and regards, Lizhi On Thu, 25 Apr 2019 at 12:05, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 4/25/19 10:54 AM, Zhi Li wrote: > > > > External Email - Use Caution > > > > 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. > In that case, the signs are flipped (ie, instead of having a column of > ones, you get a column of +1 and -1, the sign being randomly permuted). > > > > 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? > As the name implies, the CFT is used to form the cluster. Think of you > sig map as a landscape with mountains and valleys. If you were to fill > the landscape with water, you'd get some islands. The number and size > would depend on how high the water was. If you think of each island as a > cluster, then the water level is the CFT. In a purely random landscape, > some islands would form purely by chance. The propbablility of getting > an island (cluster) of a certain size or bigger is the CWP. You have to > choose the CFT. The CWP is computed from permutation. > > > > 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? > If you use permutation, then you can set the FWHM to anything. The > optimal size depends on the size of your blobs. > > > > 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? > There is no reference. Usually, I look at the worst data sets and work > my way to the better data sets to determine where the threshold should be. > > > > Looking forward to your kind suggestions. > > > > Best regards, > > > > Lizhi > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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