External Email - Use Caution Dear Dr. Douglas,
Thank you so much! Best regards, Ting On Thu, Dec 5, 2019 at 11:45 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > I've attached a couple of papers > > On 12/3/19 9:24 PM, Ting Li wrote: > > > > External Email - Use Caution > > > > Dear Dr. Douglas, > > > > Thank you so much. > > > > I have difficulty to understand z map is essentially an infinite # of > > subjects. > > Before smooth, there is no GLM analysis. Does the smooth include in > > the GLM process? > > > > Best regards, > > Ting > > > > On Tue, Dec 3, 2019 at 2:14 PM Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > > > > > On 12/3/2019 1:36 PM, Ting Li wrote: > >> > >> 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?) > >> > > The Z is essentailly an infinite # of subjects (it is just a > > single map). > >> > >> * 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? ) > >> > > The GLM analysis, from the residual. > >> > >> * threshold z map (Does it mean a GLM analysis so we can have > >> threshold z map?) > >> > > No, the z-map is synthesized directly > > > > The simulation is done in mri_glmfit-sim and in mri_mcsim. > > > >> 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! > > I don't know what you mean. > >> > >> Best regards, > >> Ting > >> > >> On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. > >> <dgr...@mgh.harvard.edu <mailto: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 <mailto: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). > >>>> > >>>> ClusterwiseCorrection for Multiple Comparisons > >>>> To perform a cluster-wise correction for multiple > >>>> comparisons, we will run a simulation. The simulation > >>>> isa way to get a measure of the distribution of the > >>>> maximum cluster size under the _null __hypothesis_. > >>>> This isdone 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 > >>>> <mailto: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 list > >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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