External Email - Use Caution Dear Dr. Douglas,

Thank you so much for all the answers. I have two more questions. 1, When the Monte Carlo simulation is doing, how does one simulation is done? - synthesize z map (synthesize z map for how many subjects?) - smooth z map (You have mentioned the FWHM comes from an estimate from the residuals of the analysis, which analysis? or the way we process the real data with the command mris_preproc with FWHM value? ) - threshold z map (Does it mean a GLM analysis so we can have threshold z map?) 2, When we reference to the CSD files in freesurfer, will it correct the cluster size p-value based on DOF (degree of freedom), like the t-ratios table including a DOF? Thanks a lot! Best regards, Ting On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Correct. This is no different than, eg, a t-test. Look in the back of a > stats book from the 1950s and you will find a table of t-ratios and > corresponding p-values. Obviously, they did not have access to any of the > data being analyzed today:), but the tables are still valid. > > On 12/2/2019 2:03 PM, Ting Li wrote: > > External Email - Use Caution > Dear Dr. Douglas, > > Thank you so much for your detailed response. > > The simulation here is to get the probability of a maximum cluster that > size or larger in the cached CSD files. It checks the probability of the > cluster size but have nothing to do with the analysis metrics that I have > used. Do I understand correctly? > > Best regards, > Ting Li > > On Mon, Dec 2, 2019 at 11:57 AM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> >> >> On 12/2/2019 11:58 AM, Ting Li wrote: >> >> External Email - Use Caution >> Dear Dr. Douglas, >> >> Thank you so much for your quick response! You saved my half life. >> >> From the introduction of clusterwise correction for multiple comparisons, >> I have a few questions. >> >> 1, What is the null hypothesis here ? >> >> In the tutorial, the null hypothesis is that there is no effect of age >> (age slope = 0) >> >> 2, What is a z map? Do you mean synthesize cortical datasets? >> >> A z-map is just a map where all the values are from a gaussian >> distribution with mean=0 and stddev=1. This just assigns a random z-value >> to each vertex on fsaverage >> >> 3. Smooth z map, what FWHM do you use, if it is not consistent with my >> FWHM, how will it affect the results? >> >> The FWHM comes from an estimate from the residuals of the analysis. The >> residuals are everything that does not fit the linear model and represent >> noise. We use the residuals to estimate the underlying smoothness (FWHM), >> >> 4, Threshold z map, what does level mean? Does it mean the vertex p-value? >> >> Basically, it is the vertex p-value, but we use the "sig" = -log10(p). >> You also have to specify the sign. If you have an a priori hypothesis about >> the direction, then you can specify pos (positive) or neg (negative). If >> you do not have an a priori hypothesis, then use abs (for absolute, for an >> unsigned test). >> >> >> Clusterwise Correction for Multiple Comparisons >> To perform a cluster-wise correction for multiple comparisons, we will run >> a simulation. The simulation is a way to get a measure of the distribution >> of the maximum cluster size under the *null **hypothesis*. This is done >> by iterating over the following steps: >> 1. Synthesize a z map >> 2. Smooth z map (using residual FWHM) >> 3. Threshold z map (level and sign) >> 4. Find clusters in thresholded map >> 5. Record area of maximum cluster >> 6. Repeat over desired number of iterations (usually > 5000) >> >> Thank you so much! >> >> Best regards, >> Ting >> >> On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. < >> dgr...@mgh.harvard.edu> wrote: >> >>> That will use the pre-computed ("cached") CSD files distributed with >>> FreeSurfer. This used 10,000 iterations. >>> >>> On 12/1/2019 11:34 PM, Ting Li wrote: >>> >>> External Email - Use Caution >>> Dear Freesurfer Expert: >>> >>> I have used the simulation code as show below: >>> >>> mri_glmfit-sim \ >>> --glmdir lh.gender_age.glmdir \ >>> --cache 4 neg \ >>> --cwp 0.05\ >>> --2spaces >>> >>> My question is how many iterations are done during this simulation? I >>> didn’t specify the iteration number. >>> >>> Why I didn’t have the csd file? >>> >>> Thanks a lot for your response! >>> >>> Best regards, >>> Ting >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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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