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
