oh, thanks Zeke for catching that Bruce On Wed, 4 Mar 2015, Z K wrote:
> Hi Gabriela, > > You might have a typo. Its "set_current_threshold_from_percentile" not > "set_threshold_from_percentile" as you have in your email. > > -Zeke > > On 03/04/2015 11:07 AM, Bruce Fischl wrote: >> you would need to include parameters, but that doesn't explain your error. >> What version of tksurfer are you using? It is probably too old >> >> On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: >> >> > Hi Bruce, >> > >> > I tried using the command set_threshold_from_percentile as a tcl script >> > but I got the following error: >> > >> > tksurfer: run tcl script: threshold.tcl >> > invalid command name "set_threshold_from_percentile"% >> > >> > Do I have to add values to the tcl command as well? >> > ________________________________________ >> > From: freesurfer-boun...@nmr.mgh.harvard.edu >> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> > [fis...@nmr.mgh.harvard.edu] >> > Sent: Wednesday, March 04, 2015 10:26 AM >> > To: Freesurfer support list >> > Subject: Re: [Freesurfer] tksurfer overlay threshold >> > >> > 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 >> > >> > >> > >> > _______________________________________________ >> > 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 >> >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
