[Freesurfer] problems on installing freesurfer
Greetings, after following the instructions in the Freesurfer-Wiki step by step i still can't run Freesurfer properly... in example: after tksurfer bert rh pial the following error is prompted: tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory all pathes and environment variables are set according to the instructions and all scripts are sourced. i'm running a Debian 3.1 on a i686 machine. .license-File is in place, too. please help! thanks a lot. Marcel Weiß Max Planck Institute for Human Cognitive and Brain Science Student at the Leipzig University of Appied Sciences ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical surface measurement.
yes, you can manually draw them in tksurfer, save them as a label file, then specify the label with -l label file name to mris_anatomical_stats. cheers, Bruce On Wed, 19 Apr 2006, Goradia, Dhruman D wrote: Hello All, Is it possible to find ROI based cortical surface measures using freesurfer? I am interested in manually tracing ROI and then obtaining thickness, surface area and curvature measures for the ROI. Is there a way to do this in freesurfer? Thank you -Dhruman ___ 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] problems on installing freesurfer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 If you have root access, try apt-get update apt-cache search libglut | more Depending on that result, try apt-get install libglut?? I might be more complicated that that, however. You might need help with setup of the XFree86 or Xorg window system to install the right drivers for your video card and setup the config correctly. The installation of OpenGL with software rendering is easier than with direct rendering, but the latter is faster. Best, Darren [EMAIL PROTECTED] wrote: Greetings, after following the instructions in the Freesurfer-Wiki step by step i still can't run Freesurfer properly... in example: after tksurfer bert rh pial the following error is prompted: tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory all pathes and environment variables are set according to the instructions and all scripts are sourced. i'm running a Debian 3.1 on a i686 machine. .license-File is in place, too. please help! thanks a lot. Marcel Weiß Max Planck Institute for Human Cognitive and Brain Science Student at the Leipzig University of Appied Sciences ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself. Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFERmylxaCYN7qs0v4RAo1tAKCBCp1p29wOcW7hEJqrx+oifpXWiQCfTCmq KeVXKMwHUglx06REM/jLfq4= =wj45 -END PGP SIGNATURE- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister segmentation fault
Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan = subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: prefixz.bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister segmentation fault
Did you mean to use tkregister2? tkregister has not been used in years (we should actually remove it from the dist). doug Sungeun Kim wrote: Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan = subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: prefixz.bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister segmentation fault
Thank you for the quick answer. I am trying to know how to use tkregister2, but I would like to know why the latest tkregister suddenly doesn't work. Sungeun. Doug Greve wrote: Did you mean to use tkregister2? tkregister has not been used in years (we should actually remove it from the dist). doug Sungeun Kim wrote: Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan = subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: prefixz.bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ 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] tkregister segmentation fault
tkregister2 is the latest. Have you been using tkregister? Sungeun Kim wrote: Thank you for the quick answer. I am trying to know how to use tkregister2, but I would like to know why the latest tkregister suddenly doesn't work. Sungeun. Doug Greve wrote: Did you mean to use tkregister2? tkregister has not been used in years (we should actually remove it from the dist). doug Sungeun Kim wrote: Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan = subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: prefixz.bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister segmentation fault
Yes, I have been using tkregister and I am not familiar with tkregister2. Doug Greve wrote: tkregister2 is the latest. Have you been using tkregister? Sungeun Kim wrote: Thank you for the quick answer. I am trying to know how to use tkregister2, but I would like to know why the latest tkregister suddenly doesn't work. Sungeun. Doug Greve wrote: Did you mean to use tkregister2? tkregister has not been used in years (we should actually remove it from the dist). doug Sungeun Kim wrote: Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan = subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: prefixz.bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ 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
