Phew!
> On Mar 4, 2015, at 5:05 PM, Hirsch, Gabriella > <gabriella_hir...@meei.harvard.edu> wrote: > > It works. I will play with this a bit. Thank you! > > > Gabriella > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, March 04, 2015 4:42 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > you need it to be: > > % sclv_set_current_threshold_from_percentile .7 .8 .9 > > or something like taht > >> On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: >> >> OK, I tried that, and it does load however I get this message in the >> terminal: >> >> tksurfer: run tcl script: threshold.tcl Wrong # args: >> sclv_set_current_threshold_from_percentile thresh mid slope% >> >> Also, the threshold continues to be the same as the default.... >> >> Thanks! >> Gabriella >> ________________________________________ >> 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 4:07 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] tksurfer overlay threshold >> >> 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 >> >> >> >> _______________________________________________ >> 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
