External Email - Use Caution For something released on CentOS4 like the 5.0.0 release mentioned in your email, you are probably better off running CentOS4 in a VM or container which in turn is hosted on a machine running a current/supported version of Linux, e.g., Rocky8, Rocky 9, Ubuntu 22, Ubuntu 24, etc. That is the usual way to preserve such an old OS environment. The version of OpenGL or system libraries something was built against on CentOS4 back in 2011 are not expected to be backwards compatible or run on a current system with an OS some 3+ revisions newer. There are virtualbox disk image archives for Freesurfer 5.0.0 (*.vdi) files underhttps://surfer.nmr.mgh.harvard..edu/pub/dist/freesurfer/5.0.0/The complete 7.5G .vdi file is,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.0.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdiIf you have root/admin privileges to install VirtualBox on some machine, then you should be able to import that .vdi file into VirtualBox - which is likely a CentOS4 VM. I believe Freesurfer 5.0.0 will already be installed there. You could also try running the VirtualBox application on a Mac or Windows machine. - R. On Aug 7, 2024, at 19:19, Raij, Tommi A. <r...@mgh.harvard.edu> wrote:Dear Surfers, I am trying to launch tksurfer/tkmedit in the stable 5_0_0 environment in the Martinos network, but this fails with glut segmentation errors. FS version 6 tksurfer works on the same machine and data, but I need to create some figures that match version 5. We already tried with a different user and a few years older linux box, same issues. Any suggestions would be greatly appreciated! For example, is there a variable that we could set to point to an older OpenGL version? (My LD_LIBRARY_PATH has not been set, and my PATH does not include anything pointing to /usr/lib or /usr/lib64) Details: on machine rukki (locally at terminal): setenv USE_STABLE_5_0_0source /usr/local/freesurfer/nmr-stable50-envcd $MY_SUBJECTS_DIR Checking version:freesurfer...You are running this version of FreeSurfer: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 echo $FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 cp -r $FREESURFER_HOME/subjects/fsaverage $MY_SUBJECTS_DIR/.chmod -R 777 fsaverage [rukki:sphsm10-ffx] (nmr-stable5.0-env) tksurfer fsaverage lh inflated subject is fsaveragehemi is lhsurface is inflatedsurfer: current subjects dir: <$MY_SUBJECTS_DIR>surfer: not in "scripts" dir ==> using cwd for session rootsurfer: session root data dir ($session) set to:surfer: <$MY_SUBJECTS_DIR>Reading image info <$MY_SUBJECTS_DIR>/fsaverage)Reading <$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgzsurfer: Reading header info from /<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz[rukki:sphsm10-ffx] (nmr-stable5.0-env) .... after which there is no screen output. The file xdebug_tksurfer was generated: [rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tksurfer SegfaultInitializing glutxDebug stack (length: 1) 00: 00: Initializing glut SegfaultInitializing glut[rukki:sphsm10-ffx] (nmr-stable5.0-env) [rukki:sphsm10-ffx] (nmr-stable5.0-env) echo $DISPLAY:3 setenv DISPLAY :0 does not fix the issue (results in GLUT: Fatal Error in tksurfer.bin: could not open display: 0) I also tried fsaverage4, fsaverage5, fsaverage6, and bert, copied from the same folder into my $SUBJECTS_DIR, same result. The issue is not specific to tksurfer: tkmedit -f fsaverage/mri/T1.mgz
===================================ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... :[rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tkmedittkmedit started: Wed Aug 7 16:54:21 2024 tkmedit.bin -f fsaverage/mri/T1.mgz $Id: tkmedit.c,v 1.341..2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5_0_0 $Set user home dir to ($MY_SUBJECTS_DIR)Set subject home dir to fsaverage/mri/T1.mgz SegfaultImporting volume with MRIreadxDebug stack (length: 5) 04: Volm_ImportData( this=0x3447db0, isSource=./fsaverage/mri/T1.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=fsaverage/mri/T1.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=tkmedit.bin ) 02: Loading volume fsaverage/mri/T1.mgz 01: main() 01: Parsing command line arguments 00: 00: [rukki:sphsm10-ffx] (nmr-stable5.0-env) My OpenGL version:[rukki:sphsm10-ffx] (nmr-stable5.0-env) glxinfo | grep "OpenGL version" OpenGL version string: 4.6.0 NVIDIA 550.54.14The other machine we tried had OpenGL version 4.6.0 NVIDIA 535.54.03 Thank you! Best regards, Tommi --- Tommi Raij, MD, PhDDirector, TMS Clinical Research MGH/MIT Athinoula A. Martinos Center for Biomedical ImagingBldg 149, 13th stCharlestown, MA 02129 _______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer
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