The log file ends abruptly. Try the following mri_glmfit-sim --debug --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg |& tee doug.log
and send me doug.log doug On 08/11/2015 07:02 AM, pablo najt wrote: > Thanks. Sorry but I am not being able to figure it out yet. Basically > I am not getting the expected outcome. > So I thought to give you an idea of how I am running permutations. > > mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 > --sim-sign neg > > And I am attaching a snapshot of the output files and the log of > mdi_glmfit-sim. > At this stage I am wondering whether in order to run permutation it is > required use as input the output from fsgd rather than qdec, because > my input is from qdec. Would this make any difference? > Thanks. > Pablo > > > Date: Mon, 10 Aug 2015 11:13:13 -0400 > > From: gr...@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Permutation output > > > > It is the same thing, but the permutation output will have the name you > > gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) > > > > On 08/10/2015 05:54 AM, pablo najt wrote: > > > Thank you Doug. > > > I run permutations with mdi_glmfit-sim --sim perm. Would you be able > > > to advice on the output and how to open the permutation outputs? The > > > tutorial instructs on how to open the *.summary file for the summary > > > of clusters and *.sig.cluster.mgh the cluster corrected map, but not > > > the permutation output. > > > Thank you, > > > Pablo > > > > > > > ------------------------------------------------------------------------ > > > Date: Fri, 7 Aug 2015 10:53:55 -0400 > > > From: gr...@nmr.mgh.harvard.edu > > > To: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec > > > > > > You can try permutation, though it is often more constraining than > > > those other two options. To do this, you'll need to run > mri_glmfit-sim > > > from the command line using the --sim perm option. Run it with --help > > > to get examples > > > > > > On 8/7/15 6:59 AM, pablo najt wrote: > > > > > > Dear FS experts, > > > I have a question about running corrections for multiple > > > comparisons. I am finding a fairly large cluster analyzing 2 > > > groups on sulcal depth. However when I tried FDR or cluster wise > > > correction the results do not seem to survive. As the result is on > > > the region I was predicting I want to make sure there are no other > > > options for correcting for multiple comparisons. I am including a > > > figure of my result to give you an idea of the size of the > > > cluster. Do you have any suggestions for trying alternative ways > > > of correcting? > > > Thank you in advance, > > > Pablo > > > > > > > > > > > > _______________________________________________ > > > 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 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 > > > _______________________________________________ > 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
