Re: [Freesurfer] Problem filling labels
Hi, I just wanted to add something to this discussion. I have in my lab, a Mac running 10.3.9 and when I run freesurfer on that I do not get this error. It is slower on my Mac than on my Linux box, but this error does not occur. I don't know if this helps in anyway, but I wanted to let you all know. Thanks so much. >Xander On Jul 7, 2005, at 4:34 PM, <[EMAIL PROTECTED]> wrote: In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. Xander Original message Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow <[EMAIL PROTECTED]> Cc: freesurfer@nmr.mgh.harvard.edu What were your settings in the Fill dialog box? Does this always happen, or only with a specific combination of options? On Thu, 7 Jul 2005, Xander Meadow wrote: Hi, I was trying to make an ROI on an inflated surface. Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that might help? Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: Here is the file you requested: Hm, that appears to be OK. What action were you performing when you got the error? Can you send me the file: $FREESURFER_HOME/lib/tcl/tksurfer.tcl On Thu, 7 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I'm having trouble filling labels using Freesurfer version 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked through the mail archives and found that this problem has happened in the past, the post is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ msg00042.html I get the same error: Error: Wrong # args: fill_flood_from_cursor dont_cross_boundary dont_cross_label dont_cross_cmid dont_cross_fthresh use_multiple_seeds action argument I have a .xdebug_tkmedit if it would help debug this issue. Does anyone know what I can do to fix this? Thank you very much. -- Kevin Teich -- Kevin Teich ___ 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
Re: [Freesurfer] Problem filling labels
Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. >Xander Original message >Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >From: Kevin Teich <[EMAIL PROTECTED]> >Subject: Re: [Freesurfer] Problem filling labels >To: [EMAIL PROTECTED] > > >I can't duplicate this at all. Has this ever worked for you, or did it >stop working? > >Can you give me the output of > >tksurfer --version > >On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: > >> In the Fill box the one I am trying to use is "Up to and >> including boundaries" by itself, but I've also tried the other >> possible combinations in a hope that it would work. Also, >> this error always happens regardless of whatever else I've done. >> >>> Xander >> >> Original message >>> Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >>> From: Kevin Teich <[EMAIL PROTECTED]> >>> Subject: Re: [Freesurfer] Problem filling labels >>> To: Xander Meadow <[EMAIL PROTECTED]> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> >>> What were your settings in the Fill dialog box? Does this >> always happen, >>> or only with a specific combination of options? >>> >>> >>> On Thu, 7 Jul 2005, Xander Meadow wrote: >>> Hi, I was trying to make an ROI on an inflated surface. >> Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that >> might help? > Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >> Here is the file you requested: > > Hm, that appears to be OK. What action were you performing >> when you got the > error? > > > >> Can you send me the file: >> >> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >> >> >> On Thu, 7 Jul 2005 [EMAIL PROTECTED] wrote: >> >>> Hi, >>> >>> I'm having trouble filling labels using Freesurfer version >>> 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked >>> through the mail archives and found that this problem has >>> happened in the past, the post is here: >>> >>> > >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html >>> >>> I get the same error: >>> >>> Error: Wrong # args: fill_flood_from_cursor >>> dont_cross_boundary dont_cross_label dont_cross_cmid >>> dont_cross_fthresh use_multiple_seeds action argument >>> >>> I have a .xdebug_tkmedit if it would help debug this issue. >>> Does anyone know what I can do to fix this? Thank you >> very much. >> > -- > Kevin Teich > >>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem filling labels
Ah, I think the version of tksurfer you are using is much newer than the one that should be associated with the script. What do you get if you try: tksurfer --all-info On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. Xander Original message Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: [EMAIL PROTECTED] I can't duplicate this at all. Has this ever worked for you, or did it stop working? Can you give me the output of tksurfer --version On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. Xander Original message Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow <[EMAIL PROTECTED]> Cc: freesurfer@nmr.mgh.harvard.edu What were your settings in the Fill dialog box? Does this always happen, or only with a specific combination of options? On Thu, 7 Jul 2005, Xander Meadow wrote: Hi, I was trying to make an ROI on an inflated surface. Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that might help? Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: Here is the file you requested: Hm, that appears to be OK. What action were you performing when you got the error? Can you send me the file: $FREESURFER_HOME/lib/tcl/tksurfer.tcl On Thu, 7 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I'm having trouble filling labels using Freesurfer version 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked through the mail archives and found that this problem has happened in the past, the post is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html I get the same error: Error: Wrong # args: fill_flood_from_cursor dont_cross_boundary dont_cross_label dont_cross_cmid dont_cross_fthresh use_multiple_seeds action argument I have a .xdebug_tkmedit if it would help debug this issue. Does anyone know what I can do to fix this? Thank you very much. -- Kevin Teich -- Kevin Teich -- Kevin Teich -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem filling labels
>freesurfer_alpha/bin/tksurfer --all-info ProgramName: tksurfer ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v 1.61 2004/01/05 20:36:23 fischl Exp $ User: xmeadow Machine: andrew Platform: Linux PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC CompilerVersion: 29600 >Xander On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote: Ah, I think the version of tksurfer you are using is much newer than the one that should be associated with the script. What do you get if you try: tksurfer --all-info On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. Xander Original message Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: [EMAIL PROTECTED] I can't duplicate this at all. Has this ever worked for you, or did it stop working? Can you give me the output of tksurfer --version On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. Xander Original message Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow <[EMAIL PROTECTED]> Cc: freesurfer@nmr.mgh.harvard.edu What were your settings in the Fill dialog box? Does this always happen, or only with a specific combination of options? On Thu, 7 Jul 2005, Xander Meadow wrote: Hi, I was trying to make an ROI on an inflated surface. Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that might help? Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: Here is the file you requested: Hm, that appears to be OK. What action were you performing when you got the error? Can you send me the file: $FREESURFER_HOME/lib/tcl/tksurfer.tcl On Thu, 7 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I'm having trouble filling labels using Freesurfer version 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked through the mail archives and found that this problem has happened in the past, the post is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ msg00042.html I get the same error: Error: Wrong # args: fill_flood_from_cursor dont_cross_boundary dont_cross_label dont_cross_cmid dont_cross_fthresh use_multiple_seeds action argument I have a .xdebug_tkmedit if it would help debug this issue. Does anyone know what I can do to fix this? Thank you very much. -- Kevin Teich -- Kevin Teich -- Kevin Teich -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem filling labels
Hi, I just opened up freesurfer and did some stuff and I got the following in the logs: surfer: using interface /opt/freesurfer_alpha/lib/tcl/tksurfer.new.tcl The /opt/freesurfer_alpha is correct, but I'm not sure what the tksurfer.new.tcl is. Inside freesurfer_alpha/lib I've got a tcl and tcl.new directory. Iniside those folders I've got: tcl.new/tksurfer.new.tcl tcl.new/tksurfer.tcl tcl/tksurfer.new.tcl.020617 tcl/tksurfer.tcl.020318 tcl/tksurfer.tcl tcl/tksurfer.tcl.040219 tcl/tksurfer.new.tcl tcl/tksurfer.tcl.020107 tcl/tksurfer.tcl.120400 But I don't know which of these I should be using. Is there a way I can check which of these is the correct one? Also, in which preference file to I tell Freesurfer to look at the correct tksurfer.tcl file? Thanks very much. >Xander Original message >Date: Fri, 8 Jul 2005 17:35:18 -0400 (EDT) >From: Kevin Teich <[EMAIL PROTECTED]> >Subject: Re: [Freesurfer] Problem filling labels >To: Xander Meadow <[EMAIL PROTECTED]> > > >Actually, I just veried that those are the correct versions to be used >together. > >The only other thing I can think of is that the binary is finding a >different version of the script. When you run tksurfer, look for a line of >output that looks like: > >surfer: using interface .../tksurfer.tcl > >and make sure the .../ part is $FREESURFER_HOME/lib/tcl. Then make sure >that 'which tksurfer' is pointing to the same $FREESURFER_HOME >installation. > > >On Fri, 8 Jul 2005, Xander Meadow wrote: > >> I'm not entirely sure where we got our current version from. If the easiest >> thing to do would be just e-mail me the new script then I am definitely in >> favor of that. I have other machines with freesurfer on them, and it's >> likely they all have this problem, would the easiest thing to do, be to just >> download a new fresh copy of freesurfer from the freesurfer website? But, >> please if it's not too much trouble, send me the new script so I can install >> that and start drawing. Thank you again so much for helping me with this. >> >> >>> Xander >> >> On Jul 8, 2005, at 3:39 PM, Kevin Teich wrote: >> >>> >>> Yes, that version is from 2004, while the script file you're using is from >>> 2003. Did you get a new version from us at some point? If so, you should've >>> gotten a corresponding tksurfer.tcl file. If not, I can give you one. >>> >>> On Fri, 8 Jul 2005, Xander Meadow wrote: >>> > freesurfer_alpha/bin/tksurfer --all-info ProgramName: tksurfer ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v 1.61 2004/01/05 20:36:23 fischl Exp $ User: xmeadow Machine: andrew Platform: Linux PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC CompilerVersion: 29600 > Xander On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote: > Ah, I think the version of tksurfer you are using is much newer than the > one that should be associated with the script. What do you get if you > try: > tksurfer --all-info > On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: >> Hi, >> It used to work in the past, but I don't know what might have >> changed. The machines run uptodate each night to stay current >> with Redhat patches, but I'm not sure what might have been >> updated right before this stopped working. As for tksurfer >> --version >> freesurfer_alpha/bin/Linux/tksurfer --version >> $ >> I'm not sure what the means though, as it's not a number, just >> the dollar sign. Does this give you any clues? Thanks so >> much for helping me out with this. >>> Xander >> Original message >>> Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >>> From: Kevin Teich <[EMAIL PROTECTED]> >>> Subject: Re: [Freesurfer] Problem filling labels >>> To: [EMAIL PROTECTED] >>> I can't duplicate this at all. Has this ever worked for you, >> or did it >>> stop working? >>> Can you give me the output of >>> tksurfer --version >>> On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've >> done. > Xander Original message > Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) > From: Kevin Teich <[EMAIL PROTECTED]> > Subject: Re: [Freesurfer] Problem filling labels > To: Xander Meadow <[EMAIL PROTECTED]> > Cc: freesurfer@nmr.mgh.harvard.edu > What were your settings in the Fill dialog box? Does this always happen, > or only with a specific combination of options? > On Thu, 7 Jul 2005, Xander Meadow wrote: >> Hi, >> I was trying to make an ROI on an in
Re: [Freesurfer] Problem filling labels
Yes, delete tksurfer.new.tcl. We stopped using tksurfer.new.tcl a while before that release and removed it from the distribution, but unfortunately, our upgrade script did not erase it. So you probably upgraded an old installation with the 2004 version, and it didn't remove the old tksurfer.new.tcl. tksurfer is hardcoded to first look for and use tksurfer.new.tcl, then tksurfer.tcl. This is for 'historical reasons'. On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I just opened up freesurfer and did some stuff and I got the following in the logs: surfer: using interface /opt/freesurfer_alpha/lib/tcl/tksurfer.new.tcl The /opt/freesurfer_alpha is correct, but I'm not sure what the tksurfer.new.tcl is. Inside freesurfer_alpha/lib I've got a tcl and tcl.new directory. Iniside those folders I've got: tcl.new/tksurfer.new.tcl tcl.new/tksurfer.tcl tcl/tksurfer.new.tcl.020617 tcl/tksurfer.tcl.020318 tcl/tksurfer.tcl tcl/tksurfer.tcl.040219 tcl/tksurfer.new.tcl tcl/tksurfer.tcl.020107 tcl/tksurfer.tcl.120400 But I don't know which of these I should be using. Is there a way I can check which of these is the correct one? Also, in which preference file to I tell Freesurfer to look at the correct tksurfer.tcl file? Thanks very much. Xander Original message Date: Fri, 8 Jul 2005 17:35:18 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow <[EMAIL PROTECTED]> Actually, I just veried that those are the correct versions to be used together. The only other thing I can think of is that the binary is finding a different version of the script. When you run tksurfer, look for a line of output that looks like: surfer: using interface .../tksurfer.tcl and make sure the .../ part is $FREESURFER_HOME/lib/tcl. Then make sure that 'which tksurfer' is pointing to the same $FREESURFER_HOME installation. On Fri, 8 Jul 2005, Xander Meadow wrote: I'm not entirely sure where we got our current version from. If the easiest thing to do would be just e-mail me the new script then I am definitely in favor of that. I have other machines with freesurfer on them, and it's likely they all have this problem, would the easiest thing to do, be to just download a new fresh copy of freesurfer from the freesurfer website? But, please if it's not too much trouble, send me the new script so I can install that and start drawing. Thank you again so much for helping me with this. Xander On Jul 8, 2005, at 3:39 PM, Kevin Teich wrote: Yes, that version is from 2004, while the script file you're using is from 2003. Did you get a new version from us at some point? If so, you should've gotten a corresponding tksurfer.tcl file. If not, I can give you one. On Fri, 8 Jul 2005, Xander Meadow wrote: freesurfer_alpha/bin/tksurfer --all-info ProgramName: tksurfer ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v 1.61 2004/01/05 20:36:23 fischl Exp $ User: xmeadow Machine: andrew Platform: Linux PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC CompilerVersion: 29600 Xander On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote: Ah, I think the version of tksurfer you are using is much newer than the one that should be associated with the script. What do you get if you try: tksurfer --all-info On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. Xander Original message Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: [EMAIL PROTECTED] I can't duplicate this at all. Has this ever worked for you, or did it stop working? Can you give me the output of tksurfer --version On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. Xander Original message Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) From: Kevin Teich <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow <[EMAIL PROTECTED]> Cc: freesurfer@nmr.mgh.harvard.edu What were your settings in the Fill dialog box? Does this always happen, or only with a specific combination of options? On Thu, 7 Jul 2005, Xander Meadow wrote: Hi, I was trying to make a
[Freesurfer] Web tool for visualizing Talairach and MNI locations in 3D volume and on the cortical surface
Freesurfer users who are interested in viewing the location of MNI and Talairach coordinates on the cortical surface or in 3D may be interested in visiting the "Martinez Flat-Mapper" site at http://www.ebire.org/hcnlab/cortical-mapping. Entering MNI or Talairach coordinates will display them on the cortical surface in relation to average gyral anatomy and in a representative 3D brain (Colin). The cortical surface maps are averages of the left and right hemispheres of 40 subjects as viewed with equal area projections that can be centered on temporal, occipital, or frontal lobes. Three different map types are available: cortical curvature, thickness, and fiber directionality (derived from the anisotropic water diffusion). There is also a high-resolution map of average auditory cortex curvature extracted using local landmark techniques. Clicking on a location on any map will display the MNI and Talairach coordinates of the point and show its location in 3D space in the Colin brain. Conversely, clicking on any location in the Colin brain will display that point on the cortical surface maps and provide an estimate of its distance to the gray/white boundary. David L. Woods, Professor of Neurology, Dept. of Neurology,UC Davis, Chief, Clinical Neurophysiology and Chief, Research fMRI imaging, Neurology Service (127E), Building R4, VANCHCS, 150 Muir Rd., Martinez, CA 94553 Tel (925) 372-2571, Fax (925) 229-2315 Email:[EMAIL PROTECTED] Website: http://marva4.ebire.org/hcnlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
