Hi Mohamad the minmax flags allows you to set the min and max thresholds for the colorscale in tksurfer. It doesn't change any pvalues - just how they are displayed. Since you are displaying -log10(p), a min of 2 will only show pvalues that are <.01 and a max of 3 will saturate the color scale at .001.
cheers Bruce On Thu, 30 Apr 2015, Alshikho, Mohamad J. wrote: > Hi Doug, > After running FSFAST tool and correcting the results for multiple > comparisons. I want t visualize the results using the command line (AS IN > WIWKI): > > tksurfer fsaverage lh inflated -overlay > my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz -annot > ./my-glm.wls/osgm/cache.th30.pos.sig.ocn.annot -fminmax 1.3 3 > > Kindly, > I want to inquire about how to use the flag -fminmax. > > For example if I have in the file "cache.th30.pos.sig.cluster.nii.gz" two > structures and the CWP is 0.0009, 0.0001 what is the correct min max values > for the flag -fminmax. > > In wiki they mentioned: > > -fminmax 2 3 : threshold set to 2 (p<.01), saturation to 3 (p<.001) > > Is this means that increasing the min value drive P value to be lower ? Is > there any role to calculate those values depending on the CWP for every > structure in "cache.th30.pos.sig.cluster.nii.gz" > > > Thanks, > Mohamad > _______________________________________________ > 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 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.
