Hi Han,

I think detvtx is the detected vertices (a binary vector with vertices were you can reject null after FDR). The 3rd argument (pth) is the FDR threshold.
You can compute pcor = -log10(pth)
from it and use it as a threshold when plotting the p-value map to limit the plot to only significant values.

I also recommend to concat the left and right hemi results and compute a single FDR threshold. That way you won't need different color bars for each hemisphere:

P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ];
G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ];
[detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0);
pcor = -log10(pth)

Best, Martin

On 12/31/2015 05:33 PM, Hanbyul Cho wrote:

Dear FreeSurfer Team,

My name is Han.

I am wondering how I can save the FDR2 corrected results.

I processed in MATLAB for Linear mixed effects models analysis, as follow:

[lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4)
[lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95);
lhstats01 = lme_mass_fit_Rgw(X,[1],Y,ni, lhTh01, lhRgs01, lhsphere,[],'euc','exp',4)

F_lhstats01=lme_mass_F(lhstats01,CM,4);
dvtx = lme_mass_FDR2(F_lhstats01.pval, F_lhstats01.sgn, lhcortex, 0.05, 0);
length(dvtx)
ans =  8000

In this case, I search the corrected results that were 8000 vertices.
I think the dvtx value was for saving the significant each vertex numbering label, is it right?
However, I don't know the next step for save the 8000 corrected vertices.

fs_write_fstats(F_lhstats01,mri,'%%$.mgh','sig');

I can save the whole results 'F_lhstats01' as the mgh format. However these were uncorrected results, is it right?

Could you let me know the method for saving the FDR2 corrected results as a mgh format?

Best Regards,

Han.

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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu 

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