Hi Gabriela they set the threshold so that 92% of the values are not displayed, and the color scale saturates at the 99 percentile
cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Thanks Bruce! > > I tried using the command: > > sclv_set_current_threshold_from_percentile > > The tried using the values .92, .925, .99 as noted on the wiki but I'm still > not quite sure what these percentages do in terms of setting the threshold? > > Thanks! > Gabriella > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, March 03, 2015 7:05 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > you can use the command: > > set_current_threshold_from_percentile(min, mid,max) > > which will compute the thresholds based on the histogram of values > > On Tue, 3 Mar 2015, Douglas N Greve wrote: > >> >> I'm not sure what you mean. optimal in what sense? >> doug >> >> On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: >>> Hi Fs experts, >>> >>> I had a quick question about settings thresholds of surface overlays >>> in Tksurfer. I am currently generating images of the thickness, >>> volume and surface area of individual subjects, and would like to >>> know if there are optimal minimum and maximum threshold values to be >>> set for different surfaces. For example, when overlaying thickness >>> (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 >>> (see attached); however I'm not sure this same threshold holds up in >>> the other surfaces (e.g. surface area). >>> >>> In summary, is there an optimal way to determine what this min. and >>> max. threshold should be in function of the distribution displayed in >>> the threshold window (see attached, on the left)? >>> >>> Thank you! >>> >>> Gabriella >>> >>> >>> _______________________________________________ >>> 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. > > > > > _______________________________________________ > 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
