try: sclv_set_current_threshold_from_percentile
cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Hi Bruce, > > I have been in touch with Zeke, who was kind enough to help me update my > version of Tksurfer. Unfortunately, this has not solved my problem (see > below). > > I am attaching here my command prompts in case I have missed anything; > > tksurfer subject rh inflated -overlay > /media/seagate_external/freesurfer_subjects/subject/surf/rh.thickness -tcl > threshold.tcl > > in the threshold.tcl I added the command: > > set_current_threshold_from_percentile > > When I run it, tksurfer loads my surface and overlay, but I receive the > following message in the terminal: > > tksurfer: run tcl script: threshold.tcl > invalid command name "set_current_threshold_from_percentile"% > > Any thoughts would be greatly appreciated! > > Thank you. > > Gabriella > > > > > ________________________________________ > From: Z K [zkauf...@nmr.mgh.harvard.edu] > Sent: Wednesday, March 04, 2015 2:32 PM > To: Hirsch, Gabriella > Subject: Re: [Freesurfer] tksurfer overlay threshold > > Yeah I figured that would be the case. > > Your best bet in this situation is to respond to Bruce's last email on > the Freesurfer list and say that Zeke provided you with the most recent > version of tksurfer but the command still does not work. You may want to > copy/paste your exact command and terminal output so that he's sure this > isnt a typo thing or some other small mistake. > > Sorry but that is the best I can do. I have no idea how to diagnose or > solve the issue you are encountering. > > -Zeke > > On 03/04/2015 02:00 PM, Hirsch, Gabriella wrote: >> oops! sorry. Well, good news, tksurfer is installed and now runs. bad news, >> I'm still getting the error message: >> >> tksurfer: run tcl script: threshold.tcl >> invalid command name "set_current_threshold_from_percentile"% >> ________________________________________ >> From: Z K [zkauf...@nmr.mgh.harvard.edu] >> Sent: Wednesday, March 04, 2015 1:49 PM >> To: Hirsch, Gabriella >> Subject: Re: [Freesurfer] tksurfer overlay threshold >> >> You'll need to make it executable. Type the following commands in the >> terminal window: >> >> $> cd $FREESURFER_HOME/tktools >> $> chmod a+x tksurfer* >> >> and let me know how it goes. >> >> -Zeke >> >> On 03/04/2015 01:38 PM, Hirsch, Gabriella wrote: >>> Still having issues calling it up - I noticed the tksurfer.bin is labeled >>> as an "unknown" file type as opposed to "program" like tkmedit.bin. Might >>> this be the reason it isn't being recognized? >>> >>> >>> Gabriella >>> >>> >>> -----Original Message----- >>> From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, March 04, 2015 12:55 PM >>> To: Hirsch, Gabriella >>> Subject: Re: [Freesurfer] tksurfer overlay threshold >>> >>> Perhaps there was a miscommunication. I gave you a "tksurfer.bin" file >>> which was supposed to replace the "tksurfer.bin" you already had. The one >>> you already had should be renamed to "tksurfer.bin.orig" for backup >>> purposes. >>> >>> This time lets just do a complete reinstall of tksurfer. Please download >>> the following 3 files: >>> >>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer >>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer.bin >>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer.tcl >>> >>> And place them into your $FREESURFER_HOME/tktools directory. Be sure the >>> executable bit is set but that should already be the case: >>> >>> $> cd $FREESURFER_HOME/tktools >>> $> chmod a+x tksurfer* >>> >>> Now try again. Unfortunaly the more I look at this the more I doubt it is >>> going to resolve the *set_current_threshold* issue, but its still worth a >>> shot. >>> >>> -Zeke >>> >>> On 03/04/2015 12:39 PM, Hirsch, Gabriella wrote: >>>> We've run into a slight problem. I downloaded and replaced the old >>>> tksurfer with the new one, but now it's not recognizing it. It just says >>>> "command not found" when I call tksurfer. Is it perhaps a permissions >>>> issue? >>>> >>>> >>>> Gabriella >>>> >>>> >>>> -----Original Message----- >>>> From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] >>>> Sent: Wednesday, March 04, 2015 12:10 PM >>>> To: Hirsch, Gabriella >>>> Cc: Bruce Fischl >>>> Subject: Re: [Freesurfer] tksurfer overlay threshold >>>> >>>> Hi Gabriela, >>>> >>>> Im providing you with the most recent version of tksurfer. I have only >>>> slim hopes this will solve the issue for you, but its worth a shot. >>>> Please download the following file: >>>> >>>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cen >>>> tos6_x86_64/tksurfer.bin >>>> >>>> And place it into your $FREESURFER_HOME/tktools directory. Backup the >>>> version you already have there by renaming to tksurfer.bin.orig. Please >>>> let us know if this solves your issue or not. >>>> >>>> -Zeke >>>> >>>> On 03/04/2015 11:27 AM, Bruce Fischl wrote: >>>>> Zeke: can you get Gabriela a current version of tksurfer and the >>>>> associated tcl scripts? >>>>> >>>>> thanks >>>>> Bruce >>>>> On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: >>>>> >>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> >> >> >> >> > > > > _______________________________________________ > 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
