Should be, so long as it is the uncorrected value. Is that the CWPmax? On Mon, Oct 3, 2016 at 2:57 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> 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. > >
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