Hi, I discovered that installing Freesurfer onto my local workstation and running Tkmedit from there has resolved my issue. It doesn't explain why tkmedit is so slow when run from our server, so if you have some ideas please let me know. Thank you all for your help.
Best, Vy On Tue, Jun 3, 2014 at 12:39 PM, Vy Dinh <vydi...@gmail.com> wrote: > Thank you for your reply. All of our Freesurfer commands, including > Tkmedit are run from the servers on the RedHat Machine. We use the ssh -Y > syntax (not -X), and when I tried using -X instead, it doesn't change the > speed of tkmedit. > > Additionally, I tried copying my data to another (department's) server at > our institution and running tkmedit from there. We didn't experience any > lag here, so this suggests that our department's dedicated server is > somehow dealing with tkmedit differently. However, when our server expert > checked the CPU usage, it appears that OUR department's server is using > less RAM overall (so it if anything, our data should process more > quickly.). In other words, we can't figure out how Tkmedit is utilized by > the servers differently. > > -Vy > > > On Tue, Jun 3, 2014 at 11:13 AM, dgw <dgwake...@gmail.com> wrote: > >> Hi, >> >> What machine are you actually running tkmedit on? >> >> more specifically: >> You appear to be using a mac. Do you run tkmedit directly on the mac? >> >> or are you using ssh -X (or something like it to run it) on the Red Hat >> machines? >> >> Thanks, >> D >> >> >> On Tue, Jun 3, 2014 at 11:55 AM, Vy Dinh <vdi...@wisc.edu> wrote: >> >>> >>> Greetings Freesurfer developers, >>> >>> I'm looking for ways to improve the speed of TKMEDIT for Freesurfer 5.3. >>> Specifically, the GUI interface is abnormally slow; edits made to a voxel >>> takes 1-2 seconds to show up on the screen. Interesting, the recon-all >>> doesn't appear to be slow (as each subject has been processed within a 24 >>> hr period), so I wonder if this problem has something to do with TKMEDIT's >>> GUI & my current setup. >>> >>> Although I SSH into our server for data processing, here are the specs >>> for my local workstation: >>> >>> Mac OSX 10.9.2 >>> 2.7 GHz Intel Core i5 Determine how many cores (Apple icon >> About this >>> Mac >> More Info) >>> 4 GB 1333 MHz DDR3 >>> >>> Server Specs: >>> >>> Our App servers have 4 Xeon CPUs apiece, each with 8 cores running at >>> 2.7GHz, for a total of 32 cores (I was told that this shouldn't be the >>> cause as the point of multi-core and multi-threading is not dependent on >>> speed only). As well, each server has 94 GB of RAM. >>> >>> Our App servers mount shares via NFS from our file servers. All servers >>> are the same version of Red Hat Linux, so there is no differences >>> there. According to the server expert at our institution, the tkmedit does >>> not appear to surpass a CPU *utilization* of 8*%* of a single core, so >>> the programs running off the server should be able to utilize its maximum >>> speed. >>> >>> I am working closely with our server expert to troubleshoot this issue, >>> so any insight from the development team will be much appreciated. Thank >>> you. >>> >>> >>> Best regards, >>> >>> Vy Dinh >>> MD Candidate, Class of 2017 >>> University of Wisconsin School of Medicine and Public Health >>> >>> _______________________________________________ >>> 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 >> >> >> 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. >> >> > > > -- > Vy T.U. Dinh > Research Assistant, Neurological Sciences > Rush University Medical Center > Phone: (312) 563-3853 > Fax: (312) 563-4660 > Email: vy_d...@rush.edu > > -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health
_______________________________________________ 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.
