In the table produced by glmfit-sim, the maximum vertex-wise uncorrected -log10(p) is given. Is that enough?
On 10/03/2016 02:55 PM, Corinna Bauer wrote: > Hi all, just following up on my previous question. For the purposes of > showing uncorrected p-values <0.005 as well as the corrected results > (via mri_glmfit-sim) I would like to get the table of uncorrected > p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir > --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but > there has gone through the simulations. I would like the raw p-values > from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd > file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex > --glmdir rh.thick.noreg.sm08.glmdir > > What command would I use? > > Thanks > Corinna > > > On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer <corinna...@gmail.com > <mailto:corinna...@gmail.com>> wrote: > > Hello all, > > I would like to get a table of the uncorrected p-values to compare > with the corrected ones obtained using mri_glmfit-sim. I tried the > following, which outputs a table of clusters and their vertices, > but it does not include p-values. Is there a flag that I shoudl > include to output the p-values? > > mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi > lh --surf white --annot aparc --no-adjust --bonferroni 2 > --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot > cache.uncorr.abs.sig.ocn.annot --cwsig > cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum > cache.uncorr.abs.sig.ocn.dat > > Thanks > > corinna > > > > > _______________________________________________ > 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 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.
