I'm using freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
I'm not sure how to check the version of tksurfer specifically? ________________________________________ 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 11:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold 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
