Dear FreeSurfers,

I have a ROI that I want to correct with FDR. I found that FreeSurfer has different implementations of FDR correction and all of them give different results.

My ROI has 4205 vertices with p values between -5.0366 and 1.1673.

When I set FDR in tksurfer (MRISfdr2vwth), I get p threshold 3.8765.

According to a post in the mail archive ( https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%3A+%5BFreesurfer%5D+RE%3A+fdr+thresholds+in+tksurfer+compared+to+Nichol%27s%09function%22&o=newest&f=1 )

I should get the same results using fast_fdrthresh matlab function in the fsfast toolbox. However, I get 4.0911.

If I use lme_mass_FDR, I get 5.0911, while lme_mass_FDR2 gives 1.9501.

Where can I find MRISfdr2vwth and why MRISfdr2vwth and fast_fdrthresh don't give me the same results? Could it be that MRISfdr2vwth seems to use all the vertices in sig.map?

MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=3.8765
MRISfdr2vwth(rate=0.050000, sign=0, 1, only_marked=0) = 3.876498
surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 3.876498

I used this command in matlab: pthreshFS=fast_fdrthresh(p(maskvtx),0.05), where maskvtx=4205.

Which FDR implementation should I use? Based on other posts, lme_mass_FDR2 seems to be preferred. I am just trying to understand these functions and use them appropriately.

Thank you!

Mihaela