[Freesurfer] tkmedit cpu usage
Hi all, Is it normal for tkmedit to saturate the cpu when freesurfer is idle? We have two researchers running the tutorial, and the tkmedit process never stops crunching the cpu, no matter how long it's been since they initiated something. We're running the latest snapshot for Linux and OS/X. Thanks, Jason ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit cpu usage
> Is it normal for tkmedit to saturate the cpu when freesurfer is idle? Yes. This is fixed in the next version. -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
Hi Brian, Thanks for the e-mail. Unfortunately we are still having problems getting the graph window to appear. Here is what we have: 1) > load the y values into tksurfer to see scatter plots. We tried to load the .bfloat file as an overlay, and got this message in the log window: sclv_read_bfloat_values: error in FunD_New Not a directory 2) Here are the messages I get in the log window when loading y_doss-thickness-250lh.fsgd file (No graph window appears): INFO: ignoring tag Creator INFO: ignoring tag SmoothSteps INFO: ignoring tag SUBECTS_DIR INFO: ignoring tag SynthSeed Read one slice only. Did you put all the slices in the same directory? WARNING: Could not get the graph title. WARNING: Could not get the measurement label. WARNING: Could not get the subject name. WARNING: Could not get the data file name. ERROR: Could not get number of classes. Thanks for your help, Robert ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
Is this the most current version of FreeSurfer? What input are you giving to load the bfloat? On Thu, 3 Jun 2004, Robert D Twomey wrote: > Hi Brian, > > Thanks for the e-mail. Unfortunately we are still having problems getting the graph > window to appear. Here is what we have: > > 1) > > load the y values into tksurfer to see scatter plots. > We tried to load the .bfloat file as an overlay, and got this message in the log > window: > > sclv_read_bfloat_values: error in FunD_New > > Not a directory > > > 2) Here are the messages I get in the log window when loading > y_doss-thickness-250lh.fsgd file (No graph window appears): > > INFO: ignoring tag Creator > INFO: ignoring tag SmoothSteps > INFO: ignoring tag SUBECTS_DIR > INFO: ignoring tag SynthSeed > Read one slice only. Did you put all the slices in the same directory? > WARNING: Could not get the graph title. > WARNING: Could not get the measurement label. > WARNING: Could not get the subject name. > WARNING: Could not get the data file name. > ERROR: Could not get number of classes. > > > Thanks for your help, > > Robert > > > > ___ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
Thanks for your prompt response. > Is this the most current version of FreeSurfer? We have the 07-24-2003 version, however I am sure that we saw this working with this version of Freesurfer last summer. If possible we would prefer to stick with our current version and avoid updating and re-installation. > What input are you giving to load the bfloat? In tksurfer File->Load Overlay, we specified the file y_doss-thickness-250lh_000.bfloat Robert - Original Message - From: Kevin Teich <[EMAIL PROTECTED]> Date: Thursday, June 3, 2004 3:10 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > Hi Brian, > > > > Thanks for the e-mail. Unfortunately we are still having > problems getting the graph window to appear. Here is what we have: > > > > 1) > > > load the y values into tksurfer to see scatter plots. > > We tried to load the .bfloat file as an overlay, and got this > message in the log window: > > > > sclv_read_bfloat_values: error in FunD_New > > > > Not a directory > > > > > > 2) Here are the messages I get in the log window when loading > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > INFO: ignoring tag Creator > > INFO: ignoring tag SmoothSteps > > INFO: ignoring tag SUBECTS_DIR > > INFO: ignoring tag SynthSeed > > Read one slice only. Did you put all the slices in the same > directory?> WARNING: Could not get the graph title. > > WARNING: Could not get the measurement label. > > WARNING: Could not get the subject name. > > WARNING: Could not get the data file name. > > ERROR: Could not get number of classes. > > > > > > Thanks for your help, > > > > Robert > > > > > > > > ___ > > Freesurfer mailing list > > [EMAIL PROTECTED] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kevin Teich > > > > ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
Loading with that kind of filename should work. Can you load other .bfloat data, or do you get this error whenever you try to load any .bfloat data? On Thu, 3 Jun 2004, Robert D Twomey wrote: > Thanks for your prompt response. > > > Is this the most current version of FreeSurfer? > > We have the 07-24-2003 version, however I am sure that we saw this working with this > version of Freesurfer last summer. If possible we would prefer to stick with our > current version and avoid updating and re-installation. > > > > What input are you giving to load the bfloat? > > In tksurfer File->Load Overlay, we specified the file > y_doss-thickness-250lh_000.bfloat > > > Robert > > > > - Original Message - > From: Kevin Teich <[EMAIL PROTECTED]> > Date: Thursday, June 3, 2004 3:10 pm > Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in > tksurfer > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > Hi Brian, > > > > > > Thanks for the e-mail. Unfortunately we are still having > > problems getting the graph window to appear. Here is what we have: > > > > > > 1) > > > > load the y values into tksurfer to see scatter plots. > > > We tried to load the .bfloat file as an overlay, and got this > > message in the log window: > > > > > > sclv_read_bfloat_values: error in FunD_New > > > > > > Not a directory > > > > > > > > > 2) Here are the messages I get in the log window when loading > > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > > > INFO: ignoring tag Creator > > > INFO: ignoring tag SmoothSteps > > > INFO: ignoring tag SUBECTS_DIR > > > INFO: ignoring tag SynthSeed > > > Read one slice only. Did you put all the slices in the same > > directory?> WARNING: Could not get the graph title. > > > WARNING: Could not get the measurement label. > > > WARNING: Could not get the subject name. > > > WARNING: Could not get the data file name. > > > ERROR: Could not get number of classes. > > > > > > > > > Thanks for your help, > > > > > > Robert > > > > > > > > > > > > ___ > > > Freesurfer mailing list > > > [EMAIL PROTECTED] > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > -- > > Kevin Teich > > > > > > > > > -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
> Can you load other .bfloat data, or do you get this error whenever > you try to load any .bfloat data? I tried a number of other files and got the same error in all cases. 1) From the same glm analysis, on the same average7 surface: beta_doss-thickness-250-lh_000.bfloat beta_doss-thickness-250-rh_000.bfloat (in a different session with the rh surface) 2) and from a different glm analysis: y_doss-thickness-250-lh_000.bfloat (with a different average7 surface from that study) Are there any others I should try to load? > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > Thanks for your prompt response. > > > > > Is this the most current version of FreeSurfer? > > > > We have the 07-24-2003 version, however I am sure that we saw > this working with this version of Freesurfer last summer. If > possible we would prefer to stick with our current version and > avoid updating and re-installation. > > > > > > > What input are you giving to load the bfloat? > > > > In tksurfer File->Load Overlay, we specified the file y_doss- > thickness-250lh_000.bfloat > > > > > > Robert > > > > > > > > - Original Message - > > From: Kevin Teich <[EMAIL PROTECTED]> > > Date: Thursday, June 3, 2004 3:10 pm > > Subject: Re: [Freesurfer] scatter plot of multiple subjects > thickness data in tksurfer > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > Hi Brian, > > > > > > > > Thanks for the e-mail. Unfortunately we are still having > > > problems getting the graph window to appear. Here is what we > have:> > > > > > > 1) > > > > > load the y values into tksurfer to see scatter plots. > > > > We tried to load the .bfloat file as an overlay, and got > this > > > message in the log window: > > > > > > > > sclv_read_bfloat_values: error in FunD_New > > > > > > > > Not a directory > > > > > > > > > > > > 2) Here are the messages I get in the log window when > loading > > > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > > > > > INFO: ignoring tag Creator > > > > INFO: ignoring tag SmoothSteps > > > > INFO: ignoring tag SUBECTS_DIR > > > > INFO: ignoring tag SynthSeed > > > > Read one slice only. Did you put all the slices in the same > > > directory?> WARNING: Could not get the graph title. > > > > WARNING: Could not get the measurement label. > > > > WARNING: Could not get the subject name. > > > > WARNING: Could not get the data file name. > > > > ERROR: Could not get number of classes. > > > > > > > > > > > > Thanks for your help, > > > > > > > > Robert > > > > > > > > > > > > > > > > ___ > > > > Freesurfer mailing list > > > > [EMAIL PROTECTED] > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > > Kevin Teich > > > > > > > > > > > > > > > > -- > Kevin Teich > > > ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
I am loading the bfloats through tksurfer, not tkmedit, using the File->Load Overlay dialogue window. When I select a bfloat file with the browse button it fills in the full path information. - Original Message - From: Kevin Teich <[EMAIL PROTECTED]> Date: Thursday, June 3, 2004 3:56 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer > Maybe it's the case that that version of tkmedit can't load > bfloats that > way. Have you tried specifying directory and stem, i.e.: > > /path/to/data/beta_doss-thickness-250-lh > > for beta_doss-thickness-250-lh_000.bfloat? > > > > > I tried a number of other files and got the same error in all cases. > > > > 1) From the same glm analysis, on the same average7 surface: > > beta_doss-thickness-250-lh_000.bfloat > > beta_doss-thickness-250-rh_000.bfloat (in a different session > with the rh surface) > > > > 2) and from a different glm analysis: > > y_doss-thickness-250-lh_000.bfloat (with a different average7 > surface from that study) > > > > > > Are there any others I should try to load? > > > > > > > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > Thanks for your prompt response. > > > > > > > > > Is this the most current version of FreeSurfer? > > > > > > > > We have the 07-24-2003 version, however I am sure that we > saw > > > this working with this version of Freesurfer last summer. If > > > possible we would prefer to stick with our current version and > > > avoid updating and re-installation. > > > > > > > > > > > > > What input are you giving to load the bfloat? > > > > > > > > In tksurfer File->Load Overlay, we specified the file y_doss- > > > thickness-250lh_000.bfloat > > > > > > > > > > > > Robert > > > > > > > > > > > > > > > > - Original Message - > > > > From: Kevin Teich <[EMAIL PROTECTED]> > > > > Date: Thursday, June 3, 2004 3:10 pm > > > > Subject: Re: [Freesurfer] scatter plot of multiple subjects > > > thickness data in tksurfer > > > > > > > > > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > > > > > Hi Brian, > > > > > > > > > > > > Thanks for the e-mail. Unfortunately we are still > having > > > > > problems getting the graph window to appear. Here is what > we > > > have:> > > > > > > > > 1) > > > > > > > load the y values into tksurfer to see scatter plots. > > > > > > We tried to load the .bfloat file as an overlay, and got > > > this > > > > > message in the log window: > > > > > > > > > > > > sclv_read_bfloat_values: error in FunD_New > > > > > > > > > > > > Not a directory > > > > > > > > > > > > > > > > > > 2) Here are the messages I get in the log window when > > > loading > > > > > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > > > > > > > > > INFO: ignoring tag Creator > > > > > > INFO: ignoring tag SmoothSteps > > > > > > INFO: ignoring tag SUBECTS_DIR > > > > > > INFO: ignoring tag SynthSeed > > > > > > Read one slice only. Did you put all the slices in the > same > > > > > directory?> WARNING: Could not get the graph title. > > > > > > WARNING: Could not get the measurement label. > > > > > > WARNING: Could not get the subject name. > > > > > > WARNING: Could not get the data file name. > > > > > > ERROR: Could not get number of classes. > > > > > > > > > > > > > > > > > > Thanks for your help, > > > > > > > > > > > > Robert > > > > > > > > > > > > > > > > > > > > > > > > ___ > > > > > > Freesurfer mailing list > > > > > > [EMAIL PROTECTED] > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > -- > > > > > Kevin Teich > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > Kevin Teich > > > > > > > > > > > > > -- > Kevin Teich > > > ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
> I am loading the bfloats through tksurfer, not tkmedit, using the > File->Load Overlay dialogue window. Sorry about that, I was confused for a minute. I just built a version from that date and it can load a bfloat volume correctly. Can you try loading the volume in tkmedit? If it can't load there, there might be a problem with the volume itself. Another source of potential error is a mismatch between the tksurfer binary and its interface file (tksurfer.tcl); have you ever tried doing an upgrade or replaced some files in your distribution that might have caused this? You can check by getting the versions of both. Send me the output of the following commands: tksurfer --all-info head $FREESURFER_HOME/lib/tcl/tksurfer.tcl > > > > - Original Message - > From: Kevin Teich <[EMAIL PROTECTED]> > Date: Thursday, June 3, 2004 3:56 pm > Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in > tksurfer > > > Maybe it's the case that that version of tkmedit can't load > > bfloats that > > way. Have you tried specifying directory and stem, i.e.: > > > > /path/to/data/beta_doss-thickness-250-lh > > > > for beta_doss-thickness-250-lh_000.bfloat? > > > > > > > > > I tried a number of other files and got the same error in all cases. > > > > > > 1) From the same glm analysis, on the same average7 surface: > > > beta_doss-thickness-250-lh_000.bfloat > > > beta_doss-thickness-250-rh_000.bfloat (in a different session > > with the rh surface) > > > > > > 2) and from a different glm analysis: > > > y_doss-thickness-250-lh_000.bfloat (with a different average7 > > surface from that study) > > > > > > > > > Are there any others I should try to load? > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > > > Thanks for your prompt response. > > > > > > > > > > > Is this the most current version of FreeSurfer? > > > > > > > > > > We have the 07-24-2003 version, however I am sure that we > > saw > > > > this working with this version of Freesurfer last summer. If > > > > possible we would prefer to stick with our current version and > > > > avoid updating and re-installation. > > > > > > > > > > > > > > > > What input are you giving to load the bfloat? > > > > > > > > > > In tksurfer File->Load Overlay, we specified the file y_doss- > > > > thickness-250lh_000.bfloat > > > > > > > > > > > > > > > Robert > > > > > > > > > > > > > > > > > > > > - Original Message - > > > > > From: Kevin Teich <[EMAIL PROTECTED]> > > > > > Date: Thursday, June 3, 2004 3:10 pm > > > > > Subject: Re: [Freesurfer] scatter plot of multiple subjects > > > > thickness data in tksurfer > > > > > > > > > > > > > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > > > > > > > Hi Brian, > > > > > > > > > > > > > > Thanks for the e-mail. Unfortunately we are still > > having > > > > > > problems getting the graph window to appear. Here is what > > we > > > > have:> > > > > > > > > > 1) > > > > > > > > load the y values into tksurfer to see scatter plots. > > > > > > > We tried to load the .bfloat file as an overlay, and got > > > > this > > > > > > message in the log window: > > > > > > > > > > > > > > sclv_read_bfloat_values: error in FunD_New > > > > > > > > > > > > > > Not a directory > > > > > > > > > > > > > > > > > > > > > 2) Here are the messages I get in the log window when > > > > loading > > > > > > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > > > > > > > > > > > INFO: ignoring tag Creator > > > > > > > INFO: ignoring tag SmoothSteps > > > > > > > INFO: ignoring tag SUBECTS_DIR > > > > > > > INFO: ignoring tag SynthSeed > > > > > > > Read one slice only. Did you put all the slices in the > > same > > > > > > directory?> WARNING: Could not get the graph title. > > > > > > > WARNING: Could not get the measurement label. > > > > > > > WARNING: Could not get the subject name. > > > > > > > WARNING: Could not get the data file name. > > > > > > > ERROR: Could not get number of classes. > > > > > > > > > > > > > > > > > > > > > Thanks for your help, > > > > > > > > > > > > > > Robert > > > > > > > > > > > > > > > > > > > > > > > > > > > > ___ > > > > > > > Freesurfer mailing list > > > > > > > [EMAIL PROTECTED] > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > -- > > > > > > Kevin Teich > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Kevin Teich > > > > > > > > > > > > > > > > > > > -- > > Kevin Teich > > > > > > > -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
