Hi Doug, The simulation went smoothly, however, as I suspected, no clusters were detected. I wonder if you have any thoughts about my question in the previous email, regarding the uncorrected p values.
Thanks! Mihaela On Thu, May 28, 2015 at 11:09 AM, Mihaela Stefan <mikaelastep...@gmail.com> wrote: > Thanks, Doug, the command seems to work. I guess it will take a while to > finish running. > > On a different note, I have a large data set that doesn't seem to generate > corrected results. What's interesting is that the uncorrected results are > consistent with our previous findings and those from the related > literature, using smaller samples (but the technique used was VBM not > surface analysis). > > In FreeSurfer, I used FDR and Monte Carlo so far with different p values > for cluster forming threshold and clusterwise p-value. Nothing survived the > correction. Now I am trying the permutation but I'm not too optimistic. So > I was wondering if there's a way to report uncorrected p-values with a > surface analysis in FreeSurfer. I know that's possible for VBM, where some > people used uncorrected p<0.001 with a cluster size of 30 voxels or p<0.005 > with a cluster size of 60 voxels. Is there an equivalent of this in > FreeSurfer? > > Thanks! > Mihaela > > On Wed, May 27, 2015 at 5:33 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Right, strictly speaking, permutationis for orthogonal design matrices >> only, which is not the case when you have a covariate. There was a >> recent paper by Anderson Winkler "Permutation Inference for the General >> Linear Model" in NI in which he goes over various permutation methods >> for non-orthogonal designs, one of which is to pretend that it is >> orthogonal (--perm-force). I don't know whether it is appropriate for >> your design or not. >> doug >> >> >> On 05/27/2015 04:37 PM, Mihaela Stefan wrote: >> > Thanks! It seems that there was a white space. I ran the permutation >> > command but now I got another error: >> > >> > ERROR: design matrix is not orthogonal, cannot be used with permutation. >> > If this something you really want to do, run with --perm-force >> > Wed May 27 16:27:50 EDT 2015 >> > ERROR: cannot find any csd files >> > >> > I did a group difference like here (first contrast): >> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V >> > >> > Best, >> > Mihaela >> > >> > >> > On Wed, May 27, 2015 at 4:18 PM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > Are you sure there is not any white space after the backslash (\)? >> > If so, Can you run it with --debug as the first option? >> > >> > On 05/27/2015 03:39 PM, Mihaela Stefan wrote: >> > > Hello FreeSurfers, >> > > >> > > I am trying to run a clusterwise correction following this link: >> > > >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >> > > >> > > I would like to use the permutation simulation instead of Z Monte >> > > Carlo. I ran mri_glmfit-sim --help to get more information. >> > > >> > > Following an example, I ran this command: mri_glmfit-sim \ >> > > --glmdir lh.g2v1.glmdir \ >> > > --sim perm 5000 1.3 perm.neg.13 --sim-sign neg >> > > Then I got an error which says: --sim: Command not found. >> > > >> > > I tried again using the exact example in the help info: >> > mri_glmfit-sim >> > > --glmdir lh.g2v1.glmdir \ >> > > --sim mc-z 10000 3 mc-z.neg.3 --sim-sign neg >> > > However, I get the same error: --sim: Command not found. >> > > >> > > Does anyone know why I get this error? >> > > >> > > Thanks! >> > > Mihaela >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto: >> 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 Partners >> > Compliance HelpLine at >> > http://www.partners.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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >
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