Hi Gabriela did you try my suggestion to call
set_threshold_from_percentile from the tcl command line? You can also try it from the tksurfer command line with -pthresh <min> <mind> <max> where all the args should be in [0,1] cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > I'm just trying to figure out what the min. and max. threshold should be in > function of the distribution in order to obtain the most accurate > representation of the overlay data in the visualizer. Any thoughts? > > Thanks! > Gabriella > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, March 03, 2015 5:48 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tksurfer overlay threshold > > > 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 > > -- > 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. > > > > > _______________________________________________ > 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
