Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

libexpat.so.1 error
by Deane Aikins 29 May '08

29 May '08

I'm installing v4.0.4 on a CentOS 4.1 i686 computer. When I go to run tkmedit, I get an error regarding libexpat.so.1. Do I need a file that is specifically for the i686 or will a lobexpat.so.1 for i586 work? Thanks, Deane

2 1

tksurfer display broken: post re-install nvidia 9746
by Juranek, Jenifer 29 May '08

29 May '08

I re-installed the dell-nvidia driver (original with system). Some new behavior observed with bert: tksurfer bert lh pial yields a complete "bert" window (entire pial surface is displayed). However, the lower window "TkSurfer Tools" is not visible. Also, tkmedit bert norm.mgz fails to launch a display, simply returns a command prompt. I've pasted the screen output for tksurfer below: Any ideas are greatly appreciated. [jjuranek@localhost subjects]$ tksurfer bert lh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131168, faces=262332 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) Tk_Init failed: this isn't a Tk applicationunknown color name "Black" Tix_Init failed: this isn't a Tk applicationunknown color name "Black" surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl: this isn't a Tk applicationunknown color name "Black" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_InflatedVSetLoaded 0: can't read "glEnableGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0: can't read "glEnableGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded 0: can't read "glEnableGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0: can't read "glEnableGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0: can't read "glEnableGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0: can't read "glEnableGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0: can't read "glEnableGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0: can't read "glEnableGroups(mg_FieldMaskLoaded)": no such variable surfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OriginalVSetLoaded 1: can't read "glEnableGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command LblLst_SetStructures { 0 Unknown 1 G_cingularis 2 G_cuneus 3 G_frontalis_inf-pars_opercularis 4 G_frontalis_inf-pars_orbitalis 5 G_frontalis_inf-pars_triangularis 6 G_frontalis_medius 7 G_frontalis_sup-pars_lateralis 8 G_frontalis_sup-pars_medialis 9 G_frontomarginalis 10 G_hippocampi 11 G_insularis_breves 12 G_occipitalis_inf 13 G_occipitalis_medius-pars_inf 14 G_occipitalis_medius-pars_sup 15 G_occipitalis_sup 16 G_lateralis 17 G_lingualis 18 G_parahippocampi 19 G_orbitalis 20 G_paracentralis 21 G_parietalis_inf-pars_angularis 22 G_parietalis_inf-pars_supramarginalis 23 G_parietalis_sup 24 G_postcentralis 25 G_precentralis 26 G_precuneus 27 G_rectus_and_S_orbitalis_medialis 28 G_rectus_and_S_orbitalis_medialis2 29 G_subcentralis 30 G_supracingularis 31 G_temporalis_transversalis 32 G_temporalis_inf 33 G_temporalis_medius 34 G_temporalis_sup-pars_lateralis 35 G_temporalis_sup-planum_polare 36 G_temporalis_sup-planum_temporale 37 Plica_falciformis 38 Polus_occipitalis 39 Polus_temporalis 40 S_temporalis_transversalis 42 S_angularis 43 S_calcarinus 44 S_centralis_insulae_&_G_insularis_longus 46 S_centralis 47 S_cingularis 48 S_cingularis-pars_marginalis 49 S_circularis_insulae_ant 50 S_circularis_insulae_inf 51 S_circularis_insulae_sup 52 S_corpori_callosi 53 S_diagonalis 54 S_frontalis_inf 55 S_frontalis_medialis 56 S_frontalis_medius 57 S_frontalis_sup 58 S_frontomarginalis 59 S_intermedius_primus 60 S_intermedius_secundus 61 S_intracingularis 62 S_intraoccipitalis_medius 63 S_intraoccipitotemporalis_lateralis 64 S_intraparietalis 65 S_lateralis-pars_ant-ramus_horizontalis 66 S_lateralis-pars_ant-ramus_verticalis 67 S_lateralis-pars_horizontalis 68 S_lateralis-pars_post 69 S_lunatus 70 S_occipitalis_ant 71 S_occipitalis_inf 72 S_occipitalis_medius 73 S_occipitalis_sup 74 S_occipitalis_transversalis 75 S_occipitopolaris 76 S_occipitotemporalis_lateralis 77 S_occipitotemporalis_medialis 78 S_orbitales 79 S_orbitalis_lateralis 80 S_paracalcarinus 81 S_paracentralis 82 S_parietalis_transversalis 83 S_parieto_occipitalis 84 S_postcentralis 85 S_precentralis 86 S_retrocalcarinus 87 S_rhinalis 88 S_subcentralis_ant_&_post_ 89 S_suborbitalis 90 S_subparietalis 91 S_supracingularis 92 S_temporalis_inf 93 S_temporalis_sup 94 S_triangularis }: invalid command name "LblLst_SetStructures" reading white matter vertex locations... surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_WhiteVSetLoaded 1: can't read "glEnableGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command UpdateLinkedVarGroup all: invalid command name "UpdateLinkedVarGroup" % surfer: Error sending tcl command MoveToolWindow 663 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 664 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 666 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 667 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 669 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 671 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 675 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 675 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 683 684: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 691 684: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 703 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 705 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 713 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 727 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 729 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 739 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 740 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 743 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 753 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 756 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 766 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 774 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 790 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 793 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 813 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 813 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 829 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 845 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 848 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 851 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 852 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 855 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 856 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 860 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 862 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 866 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 868 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 874 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 876 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 878 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 884 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 887 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 892 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 894 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 896 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 899 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 901 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 902 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 905 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 906 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 908 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 910 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 911 693: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 916 693: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 917 692: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 919 692: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 922 691: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 923 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 926 689: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 927 689: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 928 688: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 931 687: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 932 686: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 933 686: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 934 686: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 934 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow"

1 0

Mac OS & bash-file
by MRI CDPI 29 May '08

29 May '08

Dear Freesurfers, i am a brand new user of a Mac Pro without any experience of that system. I am trying to include in the bash file the startup commands for Freesurfer, but i could find a way to save the changes in the bash file. I already tried to change the permission status of the bashrc file with chmod +w bashrc, but it is not possible, just says "Operation not permitted". Could somebody help me with this? Thanks a lot, Cheers, Thomas

1 0

problem with patch file
by Elif SIKOGLU 29 May '08

29 May '08

Hello, I am trying to flatten the occipital patch that I cut using mris_flatten. However I keep getting the following error: reading patch lh.occip.patch.3d with 1229531648 vertices (951539.4% of total) MRISreadPatch: bad vertex # (931524607) found in patch file No such file or directory I attached the lh.occip.patch.3d file. Any ideas? Thanks, PS: for the past few days I keep getting a similar error for other subjects as well during flattening or creating maps etc.

2 1

combining runs from different scans
by Elif SIKOGLU 29 May '08

29 May '08

Hello, If we have two runs of a subject in one scan and another two runs of the same subject in another scan, is it possible to combine these runs while running the analysis given we have done autoalignment during scans? Thanks,

1 0

Re: tksurfer display broken
by Dr. Glenn Lawyer 29 May '08

29 May '08

Hi, I am experiencing similar problems to Jennifer with tksurfer; the key (tksurfer) error message being surfer: ### redraw failed: no gl window open and the display showing only a thin slice of the posterior of the surface. The computer is a fresh install of RHEL 5. Matlab is NOT (yet) installed on the machine. Specifically: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.4 subjects$ sudo /sbin/lspci 01:00.0 VGA compatible controller: ATI Technologies Inc RV516 [Radeon X1300/X1550 Series] 01:00.1 Display controller: ATI Technologies Inc RV516 [Radeon X1300 Pro] (Secondary) I just yesterday updated the video driver: $ yum -y install fglrx64_7_1_0 initscripts-atidriver and auto-configed the X11 server $ aticonfig --initial=dual-head --screen-layout=right The tksurfer problem occured with the autoconfiged xorg.conf file, which is at the end of my message. Adding Section "Extensions" Option "Composite" "Disable" EndSection didn't help (I tried this only for completeness, I do not know if "composite" is an option on ATI cards). # Xorg configuration created by pyxf86config Section "ServerLayout" Identifier "Default Layout" Screen 0 "aticonfig-Screen[0]" 0 0 Screen "aticonfig-Screen[1]" RightOf "aticonfig-Screen[0]" InputDevice "Keyboard0" "CoreKeyboard" EndSection Section "Files" EndSection Section "Module" EndSection Section "Monitor" Identifier "aticonfig-Monitor[0]" Option "VendorName" "ATI Proprietary Driver" Option "ModelName" "Generic Autodetecting Monitor" Option "DPMS" "true" EndSection Section "Monitor" Identifier "aticonfig-Monitor[1]" Option "VendorName" "ATI Proprietary Driver" Option "ModelName" "Generic Autodetecting Monitor" Option "DPMS" "true" EndSection Section "Device" Identifier "Videocard0" Driver "vesa" EndSection Section "Device" Identifier "aticonfig-Device[0]" Driver "fglrx" BusID "PCI:1:0:0" EndSection Section "Device" Identifier "aticonfig-Device[1]" Driver "fglrx" BusID "PCI:1:0:0" Screen 1 EndSection Section "Screen" Identifier "Screen0" Device "Videocard0" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection Section "Screen" Identifier "aticonfig-Screen[0]" Device "aticonfig-Device[0]" Monitor "aticonfig-Monitor[0]" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection Section "Screen" Identifier "aticonfig-Screen[1]" Device "aticonfig-Device[1]" Monitor "aticonfig-Monitor[1]" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection

3 2

qdec error as already reported by William McGarry in February
by Claus Tempelmann 29 May '08

29 May '08

Hello, In February William McGarry has reported a qdec error (see original message from William below) and to fix this error a new version of fsgdfPlot.tcl was sent to him. We have not found any comment from William whether this file has actually solved his problem but we have the very same problem now and it seems that we have the most recent version of fsgdfPlot.tcl (from January 3rd 2008, we have downloaded freesurfer-Linux-rh9-stable-pub-v4.0.4 a few days ago). So, does anybody know what else could cause this error? Thanks for your help Claus ----------------------------------------------------------------------- Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany ---------- Forwarded message ---------- Date: Thu, 29 May 2008 12:27:57 +0200 From: Claus Tempelmann <Claus.Tempelmann(a)web.de> To: Claus.Tempelmann(a)Medizin.Uni-Magdeburg.DE Subject: qdec error Fri, 08 Feb 2008 13:12:13, William R Mcgarry wrote: When trying to analyze some data in qdec, after I completed recon-all -all and -qcache for the subjects in my qdec table, I get to the Display tab and pick an option under Scalar. It doesn't matter which option, as they all give me the same two errors repeatedly (forcing me to quit qdec). These are: (1) ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x87548598): TclTK error: invalid command name "vtkTemp349" invalid command name "vtkTemp349" while executing "vtkTemp349 FocusInCallback" (command bound to event) and (2) ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x8748598): TclTK error: invalid command name "vtkTemp347" invalid command name "vtkTemp347" while executing "vtkTemp347 FinishEditing" (command bound to event) Any help is greatly appreciated. Thanks. -Ryan McGarry --------------------------------------------------------------------- _______________________________________________________________________ Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220

1 0

tksurfer problems
by Lars M. Rimol 29 May '08

29 May '08

Hi, I am experiencing similar problems to Jennifer and Glenn with tksurfer; the (tksurfer) error message is: surfer: ### redraw failed: no gl window open and the display shows only a thin slice of the posterior of the surface. The computer is a fresh install of RHEL 5 on a new machine, and my university IT department has updated the OS in connection with a Matlab installation. I believe they used run "yum update". I have tried both FS v.4.0.3 and v.4.0.4. yours, LMR -- yours, LMR

1 0

Re: Freesurfer Digest, Vol 51, Issue 33
by Dr. Glenn Lawyer 29 May '08

29 May '08

Dear Paul > From: Paul Raines <raines(a)nmr.mgh.harvard.edu> > Subject: RE: [Freesurfer] tksurfer display broken: "smart" over-ride? > > Do you see any warnings (WW) or errors (EE) in your /var/log/Xorg.0.log > file? > > What does running 'glxinfo' say? > > On Wed, 28 May 2008, Juranek, Jenifer wrote: > > bash-3.2# grep WW /var/log/Xorg.0.log (WW) warning, (EE) error, (NI) not implemented, (??) unknown. (WW) fglrx: No matching Device section for instance (BusID PCI:1:0:1) found (WW) fglrx(0): Failed to open DRM connection (WW) fglrx(0): board is an unknown third party board, chipset is supported (WW) fglrx(0): No DRM connection for driver fglrx. (WW) fglrx(1): board is an unknown third party board, chipset is supported (WW) fglrx(0): *********************************************** (WW) fglrx(0): * DRI initialization failed! * (WW) fglrx(0): * (maybe driver kernel module missing or bad) * (WW) fglrx(0): * 2D acceleraton available (MMIO) * (WW) fglrx(0): * no 3D acceleration available * (WW) fglrx(0): ********************************************* * (WW) fglrx(0): Failed to set up write-combining range (0xc0000000,0x8000000) (WW) fglrx(0): Textured Video not supported without DRI enabled. (WW) fglrx(0): Option "VendorName" is not used (WW) fglrx(0): Option "ModelName" is not used (WW) fglrx(1): DRI initialization on primary screen failed. (WW) fglrx(1): *********************************************** (WW) fglrx(1): * DRI initialization failed! * (WW) fglrx(1): * (maybe driver kernel module missing or bad) * (WW) fglrx(1): * 2D acceleraton available (MMIO) * (WW) fglrx(1): * no 3D acceleration available * (WW) fglrx(1): ********************************************* * (WW) fglrx(1): Failed to set up write-combining range (0xc8000000,0x8000000) (WW) fglrx(1): Textured Video not supported without DRI enabled. (WW) <default pointer>: No Device specified, looking for one... bash-3.2# grep EE /var/log/Xorg.0.log (WW) warning, (EE) error, (NI) not implemented, (??) unknown. (II) Loading extension MIT-SCREEN-SAVER (EE) fglrx(0): atiddxDriScreenInit failed, GPS not been initialized. (EE) fglrx(1): DRI initialization for 2nd screen failed - aborting! bash-3.2# glxinfo name of display: :0.0 display: :0 screen: 0 direct rendering: No server glx vendor string: SGI server glx version string: 1.2 server glx extensions: GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_EXT_texture_from_pixmap, GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_hyperpipe, GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_MESA_copy_sub_buffer client glx vendor string: SGI client glx version string: 1.4 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_allocate_memory, GLX_MESA_swap_control, GLX_MESA_swap_frame_usage, GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group, GLX_EXT_texture_from_pixmap GLX version: 1.2 GLX extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_EXT_texture_from_pixmap OpenGL vendor string: Mesa project: www.mesa3d.org OpenGL renderer string: Mesa GLX Indirect OpenGL version string: 1.2 (1.5 Mesa 6.5.1) OpenGL extensions: GL_ARB_depth_texture, GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_shadow_ambient, GL_ARB_texture_border_clamp, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two, GL_ARB_texture_rectangle, GL_ARB_transpose_matrix, GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_func_separate, GL_EXT_blend_logic_op, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_copy_texture, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_object, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_point_parameters, GL_EXT_polygon_offset, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_wrap, GL_EXT_subtexture, GL_EXT_texture, GL_EXT_texture3D, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_lod_bias, GL_EXT_texture_object, GL_EXT_texture_rectangle, GL_EXT_vertex_array, GL_APPLE_packed_pixels, GL_ATI_texture_env_combine3, GL_ATI_texture_mirror_once, GL_ATIX_texture_env_combine3, GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate, GL_MESA_pack_invert, GL_MESA_ycbcr_texture, GL_NV_blend_square, GL_NV_point_sprite, GL_NV_texgen_reflection, GL_NV_texture_rectangle, GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod, GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SGIX_shadow_ambient, GL_SUN_multi_draw_arrays visual x bf lv rg d st colorbuffer ax dp st accumbuffer ms cav id dep cl sp sz l ci b ro r g b a bf th cl r g b a ns b eat ---------------------------------------------------------------------- 0x23 24 tc 0 24 0 r y . 8 8 8 0 0 16 0 0 0 0 0 0 0 None 0x24 24 tc 0 24 0 r y . 8 8 8 0 0 16 8 16 16 16 0 0 0 None 0x25 24 tc 0 32 0 r y . 8 8 8 8 0 16 8 16 16 16 16 0 0 None 0x26 24 tc 0 32 0 r . . 8 8 8 8 0 16 8 16 16 16 16 0 0 None 0x27 24 dc 0 24 0 r y . 8 8 8 0 0 16 0 0 0 0 0 0 0 None 0x28 24 dc 0 24 0 r y . 8 8 8 0 0 16 8 16 16 16 0 0 0 None 0x29 24 dc 0 32 0 r y . 8 8 8 8 0 16 8 16 16 16 16 0 0 None 0x2a 24 dc 0 32 0 r . . 8 8 8 8 0 16 8 16 16 16 16 0 0 None display: :0 screen: 1 direct rendering: No server glx vendor string: SGI server glx version string: 1.2 server glx extensions: GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_EXT_texture_from_pixmap, GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_hyperpipe, GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_MESA_copy_sub_buffer client glx vendor string: SGI client glx version string: 1.4 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_allocate_memory, GLX_MESA_swap_control, GLX_MESA_swap_frame_usage, GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group, GLX_EXT_texture_from_pixmap GLX version: 1.2 GLX extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_EXT_texture_from_pixmap OpenGL vendor string: Mesa project: www.mesa3d.org OpenGL renderer string: Mesa GLX Indirect OpenGL version string: 1.2 (1.5 Mesa 6.5.1) OpenGL extensions: GL_ARB_depth_texture, GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_shadow_ambient, GL_ARB_texture_border_clamp, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two, GL_ARB_texture_rectangle, GL_ARB_transpose_matrix, GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_func_separate, GL_EXT_blend_logic_op, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, GL_EXT_copy_texture, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_object, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_point_parameters, GL_EXT_polygon_offset, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_wrap, GL_EXT_subtexture, GL_EXT_texture, GL_EXT_texture3D, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_lod_bias, GL_EXT_texture_object, GL_EXT_texture_rectangle, GL_EXT_vertex_array, GL_APPLE_packed_pixels, GL_ATI_texture_env_combine3, GL_ATI_texture_mirror_once, GL_ATIX_texture_env_combine3, GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate, GL_MESA_pack_invert, GL_MESA_ycbcr_texture, GL_NV_blend_square, GL_NV_point_sprite, GL_NV_texgen_reflection, GL_NV_texture_rectangle, GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod, GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SGIX_shadow_ambient, GL_SUN_multi_draw_arrays visual x bf lv rg d st colorbuffer ax dp st accumbuffer ms cav id dep cl sp sz l ci b ro r g b a bf th cl r g b a ns b eat ---------------------------------------------------------------------- 0x3e 24 tc 0 24 0 r y . 8 8 8 0 0 16 0 0 0 0 0 0 0 None 0x3f 24 tc 0 24 0 r y . 8 8 8 0 0 16 8 16 16 16 0 0 0 None 0x40 24 tc 0 32 0 r y . 8 8 8 8 0 16 8 16 16 16 16 0 0 None 0x41 24 tc 0 32 0 r . . 8 8 8 8 0 16 8 16 16 16 16 0 0 None 0x42 24 dc 0 24 0 r y . 8 8 8 0 0 16 0 0 0 0 0 0 0 None 0x43 24 dc 0 24 0 r y . 8 8 8 0 0 16 8 16 16 16 0 0 0 None 0x44 24 dc 0 32 0 r y . 8 8 8 8 0 16 8 16 16 16 16 0 0 None 0x45 24 dc 0 32 0 r . . 8 8 8 8 0 16 8 16 16 16 16 0 0 None bash-3.2#

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Re: tksurfer display broken
by Dr. Glenn Lawyer 29 May '08

29 May '08

Hi, I am experiencing similar problems to Jennifer with tksurfer; the key (tksurfer) error message being surfer: ### redraw failed: no gl window open and the display showing only a thin slice of the posterior of the surface. The computer is a fresh install of RHEL 5 on a new machine, and I've run "yum update." Our university IT department also auto-updates the machines. Matlab is NOT (yet) installed on the machine. I have just installed the latest FreeSurfer and this is my first time trying to run it on this machine. Specifics: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.4 kernel: Red Hat Enterprise Linux Client (2.6.18-92.el5) subjects$ sudo /sbin/lspci 01:00.0 VGA compatible controller: ATI Technologies Inc RV516 [Radeon X1300/X1550 Series] 01:00.1 Display controller: ATI Technologies Inc RV516 [Radeon X1300 Pro] (Secondary) I just yesterday updated the video driver: $ yum -y install fglrx64_7_1_0 initscripts-atidriver and auto-configed the X11 server $ aticonfig --initial=dual-head --screen-layout=right The tksurfer problem occured with the autoconfiged xorg.conf file, which is at the end of my message. Adding Section "Extensions" Option "Composite" "Disable" EndSection didn't help (I tried this only for completeness, I do not think "composite" is an option on ATI cards). # Xorg configuration created by pyxf86config Section "ServerLayout" Identifier "Default Layout" Screen 0 "aticonfig-Screen[0]" 0 0 Screen "aticonfig-Screen[1]" RightOf "aticonfig-Screen[0]" InputDevice "Keyboard0" "CoreKeyboard" EndSection Section "Files" EndSection Section "Module" EndSection Section "Monitor" Identifier "aticonfig-Monitor[0]" Option "VendorName" "ATI Proprietary Driver" Option "ModelName" "Generic Autodetecting Monitor" Option "DPMS" "true" EndSection Section "Monitor" Identifier "aticonfig-Monitor[1]" Option "VendorName" "ATI Proprietary Driver" Option "ModelName" "Generic Autodetecting Monitor" Option "DPMS" "true" EndSection Section "Device" Identifier "Videocard0" Driver "vesa" EndSection Section "Device" Identifier "aticonfig-Device[0]" Driver "fglrx" BusID "PCI:1:0:0" EndSection Section "Device" Identifier "aticonfig-Device[1]" Driver "fglrx" BusID "PCI:1:0:0" Screen 1 EndSection Section "Screen" Identifier "Screen0" Device "Videocard0" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection Section "Screen" Identifier "aticonfig-Screen[0]" Device "aticonfig-Device[0]" Monitor "aticonfig-Monitor[0]" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection Section "Screen" Identifier "aticonfig-Screen[1]" Device "aticonfig-Device[1]" Monitor "aticonfig-Monitor[1]" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection

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