Yes, when you are running the simulation you should pass it the fwhm (new versions *force* you to pass it a fwhm when running the simulation, even if it is 0). And, yes, if you do not give it the proper fwhm (or pass 0), then it will make it more likely that clusters will be deemed significant.
doug James Porter wrote: > Thanks, Doug. Just so I'm clear: passing mri_glmfit the value in > fwhm.dat is the *proper* thing to do, and not giving the simulation > that information on the residual smoothness would cause the p-value > estimates to be biased towards letting clusters in, yes? > > --------- > Jim Porter > Graduate Student > Clinical Science & Psychopathology Research > University of Minnesota > > Douglas N Greve wrote: >> The cluster sizes/locations won't change because those are dependent >> on your actual data, not the simulation. If you change the smoothing >> level in the QDEC analysis, you will find that the cluster >> sizes/locations change. The simulation is only for computing the >> pvalues (CWP) of the clusters, and that does look like it has changed >> substantially between the two simulations. >> >> doug >> >> James Porter wrote: >>> Hi Doug- >>> >>> You can see the full logs & a screenshot of the mgh files here: >>> https://netfiles.umn.edu/xythoswfs/webui/_xy-10431983_1-t_4xQ4HIVC >>> >>> Below are the commands (full pathways removed for brevity) that I ran. >>> >>> -Jim >>> >>> >>> # mri glmfit command & fwhm listing from original qdec log >>> mri_glmfit --y 168.All.FAS.lh.qdec/y.mgh --fsgd >>> 168.All.FAS.lh.qdec/qdec.fsgd dods --glmdir 168.All.FAS.lh.qdec >>> --surf fsaverage lh --label >>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --C >>> 168.All.FAS.lh.qdec/contrasts/lh-Avg-Intercept-thickness.mat --C >>> 168.All.FAS.lh.qdec/contrasts/lh-Avg-thickness-FAS_Tot-Cor.mat >>> >>> ResidualFWHM 16.296576 >>> >>> >>> # an example of the glmfit simulation commands with smoothing >>> cd 168.All.FAS.lh.qdec/ >>> mri_glmfit --y y.mgh --C contrasts/lh-Avg-thickness-FAS_Tot-Cor.mat >>> --mask mask.mgh --sim mc-z 500 1.3 csd/mc-z.abs.p05.sim1 --sim-sign >>> abs --fwhm 16.296576 --fsgd y.fsgd --surf fsaverage lh >>> >>> >>> # command for clustering of the doubly smoothed data >>> # note: if I try to pass fwhm into mri_surfcluster, I get an error >>> that it can't be done with the 'abs' flag >>> mri_surfcluster --hemi lh --subject fsaverage --in >>> lh-Avg-thickness-FAS_Tot-Cor/sig.mgh --sum >>> lh-Avg-thickness-FAS_Tot-Cor/sig.mc-z.p001.sum --cwsig >>> lh-Avg-thickness-FAS_Tot-Cor/sig.mc-z.p001.mgh --annot aparc --thmin >>> 3 --sign abs --csd >>> csd/mc-z.abs.p001.sim10-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim1-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim2-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim3-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim4-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim5-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim6-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim7-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim8-lh-Avg-thickness-FAS_Tot-Cor.csd --csd >>> csd/mc-z.abs.p001.sim9-lh-Avg-thickness-FAS_Tot-Cor.csd >>> >>> >>> # command from the no smoothing glmfit sims >>> cd 168.All.FAS.lh.qdec/ >>> mri_glmfit --y y.mgh --C contrasts/lh-Avg-thickness-FAS_Tot-Cor.mat >>> --mask mask.mgh --sim mc-z 500 3 csd/mc-z.nosmooth.abs.p001.sim2 >>> --sim-sign abs --fwhm 0 --fsgd y.fsgd --surf fsaverage lh >>> >>> # no smoothing clustering command >>> mri_surfcluster --hemi lh --subject fsaverage --in >>> lh-Avg-thickness-FAS_Tot-Cor/sig.mgh --sum >>> lh-Avg-thickness-FAS_Tot-Cor/sig.mc-z.nosmooth.p001.sum --cwsig >>> lh-Avg-thickness-FAS_Tot-Cor/sig.mc-z.nosmooth.p001.mgh --annot >>> aparc --thmin 3 --sign abs --olab >>> FAS_168.All.FAS.lh.mc-z.nosmooth.p001 --csd >>> csd/mc-z.nosmooth.abs.p001.sim10-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim1-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim2-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim3-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim4-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim5-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim6-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim7-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd >>> csd/mc-z.nosmooth.abs.p001.sim8-lh-Avg-thickness-FAS_Tot-Cor.csd >>> --csd csd/mc-z.nosmooth.abs.p001.sim9-lh-Avg-thickness-FAS_Tot-Cor.csd >>> >>> >>> >>> Douglas N Greve wrote: >>>> Can you send your mri_glmfit and mri_surfcluster command-lines? >>>> >>>> doug >>>> >>>> James Porter wrote: >>>>> Sorry, I mistyped. To clarify, the original qdec analyses were run >>>>> on the 10mm smoothed data from qcache, and the sims were then run >>>>> with and without passing the value from fwhm.dat into the FWHM >>>>> flag in mri_glmfit. >>>>> >>>>> --------- >>>>> Jim Porter >>>>> Graduate Student >>>>> Clinical Science & Psychopathology Research >>>>> University of Minnesota >>>>> >>>>> James Porter wrote: >>>>>> I have recently run simulations with and without the FWHM flag, >>>>>> and the results were 100% identical, in both the mgh output and >>>>>> cluster summary files. From what is below, I would think that the >>>>>> results should have changed in at least some way. The original >>>>>> qdec analysis was run with 10mm smoothing, and the sims (mc-full, >>>>>> 10k) were run with and without 10mm smoothing. >>>>>> >>>>>> Is there a certain point at which one would not expect smoothing >>>>>> in the simulations to not matter? >>>>>> >>>>>> --------- >>>>>> Jim Porter >>>>>> Graduate Student >>>>>> Clinical Science & Psychopathology Research >>>>>> University of Minnesota >>>>>> >>>>>> Douglas N Greve wrote: >>>>>>> <div class="moz-text-flowed" style="font-family: -moz-fixed">1) >>>>>>> The smoother the data, the more likely a cluster will be found >>>>>>> by chance. When the data are created, they start with some >>>>>>> smoothness level. When you smooth them you add more. So you need >>>>>>> to match the total level of smoothing when you do the >>>>>>> simulations, otherwise your clusters will be way too >>>>>>> significant. mri_glmfit creates a fwhm.dat file with an estimate >>>>>>> of the total smoothness. >>>>>>> >>>>>>> 2) Just if they are nearest neighbors. There is no option to >>>>>>> tinker with this. >>>>>>> >>>>>>> 3) Vertices in the maps created by the simulation are >>>>>>> thresholded at the level you pass. This is what defines the >>>>>>> cluster. >>>>>>> >>>>>>> doug >>>>>>> >>>>>>> Dankner, Nathan (NIH/NIMH) [F] wrote: >>>>>>>> Hello all, >>>>>>>> >>>>>>>> I have a couple of questions regarding the way the cluster >>>>>>>> correction simulation in freesurfer works. I've read the wiki >>>>>>>> pages on the subject, but if I've missed something and any of >>>>>>>> this is answered elsewhere please let me know. My technical >>>>>>>> knowledge of these things is not great so I am just trying to >>>>>>>> get some background. First of all, how does smoothing the data >>>>>>>> prior to running the simulation affect the results? I've run >>>>>>>> corrections on the same data smoothed with a 10mm FWHM, and >>>>>>>> also on completely unsmoothed data, and the cluster results >>>>>>>> were different. Secondly, what determines whether vertices are >>>>>>>> neighbors or not? Is there an option to tinker with this or is >>>>>>>> it predetermined? Lastly, how do the p values of individual >>>>>>>> vertices factor into the simulation? Are they taken into >>>>>>>> account when the determination of the max cluster size under >>>>>>>> the null hypothesis is performed? Thanks in advance, >>>>>>>> >>>>>>>> Nate >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> [email protected] >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
