0.09940 and 0.10338 seem pretty close to me:). The summary file has Hi and Low which is the 95% confidence interval assuming a binomial model at the mean prob
On 9/9/2020 3:24 PM, freesurferl...@gmx.com wrote: > External Email - Use Caution > > Thanks, I was looking for the higher resolution as, from my understanding, > the p-value of a cluster is usually reported as “p =“ rather than “p <“ (but > this may be not worth the extra computational time for cluster 1). > > Just as a follow up question, what about cluster 2 for cwp0.1 and cwp0.999. > This has a CWP of 0.09940 and 0.10338 respectively. Should we be expecting > convergence by 10,000 iterations for this cluster? > > > > On 10/9/20 at 12:18 am, Douglas N. Greve wrote: > > The issue is that the chance of this event happening by chance is very > low, around 2-14 times out of 10,000. You are getting this variation > because you are only using 10000 iterations. But why would you need > higher resolution to your p-value? It will definitely be below 0.05 > needed for publication. > > On 9/8/2020 8:45 PM, Paul wrote: >> External Email - Use Caution >> >> Dear Douglas, >> Thanks for looking in this. Please see files attached. >> Also, I have used Freesurfer 5.1 for all the processing (i.e recon-all >> and editing etc) and have used Freesurfer 6.0 for the statistical >> analysis (i.e. mris_preproc, mri_surf2surf, mri_glmfit) and the patch >> version of mri_glmfit-sim (i.e >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim). >> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim> >> Kind regards, >> Paul >> *Sent:* Wednesday, September 09, 2020 at 1:01 AM >> *From:* "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp >> 0.1, --cwp 0.999 >> On 9/7/2020 10:52 PM, Paul wrote: >> >> External Email - Use Caution >> >> Dear Freesurfer Experts, >> I have few questions regarding CWP values from mri_glmfit-sim >> using --cwp 0.05, --cwp 0.1, --cwp 0.999. >> Using the 3 three commands below (A, B and C): >> A. mri_glmfit-sim --glmdir lh_status.glmdir --perm 10000 1.3 abs >> --cwp 0.05 --2spaces --bg 1 >> B. mri_glmfit-sim --glmdir lh_status.glmdir --perm 10000 1.3 abs >> --cwp 0.1 --2spaces --bg 1 >> C. mri_glmfit-sim --glmdir lh_status.glmdir --perm 10000 1.3 abs >> --cwp 0.999 --2spaces --bg 1 >> I end up with the same significant ClusterNo 1. (in terms of Max, >> VtxMax, Size(mm^2), MNIX, MNIY, MNIZ, NVtxs, WghtVtx, Annot) >> However, the CWP is 0.00040, 0.00140, and 0.00020 for A, B and C >> respetively. >> I was expected after 10,000 iterations, the CWP would be more >> closely matched or even convergent. >> Could you please let me know if this result is typical after >> 10,000 iterations? >> Also, should I be using more iterations (say 20k or more 100k?) to >> reach convergence across A, B, and C or is it usual to just report >> A, B or C? >> >> I don't understand. All you are changing is the CWP threshold? The >> final CWP value for a cluster should not be changing at all. If this >> is the case, can you send me the summary file for each? >> >> Kind regards, >> Paul >> >> _______________________________________________ >> 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 > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Mass General Brigham > Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If > the e-mail was sent to you in error but does not contain patient information, > please contact the sender and properly dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
