Hi all,
I am new to freesurfer. I just installed the freesurfer 3.0.5 to my computer (fedora core 6 x86_64). I do the steps described in the wiki for the installation and then checked whether it is working. The tkmedit works properly. However tksurfer has some problems in rendering the surface. The program works with no error :
----------------------------------------------------------------------------- "tksurfer bert lh pial" command output
[root@localhost freesurfer]# 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 Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /usr/local/freesurfer/subjects/bert/mri/transforms/talairach.xfm surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=132794, faces=265584 Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /usr/local/freesurfer/subjects/bert/surf/../mri/transforms/talairach.xfm surfer: single buffered window 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 Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl -----------------------------------------------------------------------------
but I can just see a little portion of the surface in the viewing window of tksurfer. I tried the right and left hemispheres, but the same result. I also add the image of the tksurfer window to the attachments. I guess there is a opengl rendering problem. I believe my grapics card is working properly. I also add the output of glxinfo command to the end of the mail. Do you have any suggestions for my case.
Thanks a lot in advance.
Burak Ozkalayci
------------------------------------------------------------------------------ [root@localhost freesurfer]# glxinfo name of display: :0.0 display: :0 screen: 0 direct rendering: Yes 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: ATI client glx version string: 1.3 client glx extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_ARB_get_proc_address, GLX_SGI_video_sync, GLX_ARB_multisample, GLX_ATI_pixel_format_float, GLX_ATI_render_texture GLX version: 1.2 GLX extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_ARB_multisample OpenGL vendor string: ATI Technologies Inc. OpenGL renderer string: ATI Mobility Radeon X1400 OpenGL version string: 2.0.6334 (8.34.8) OpenGL extensions: GL_ARB_multitexture, GL_EXT_texture_env_add, GL_EXT_compiled_vertex_array, GL_S3_s3tc, GL_ARB_depth_texture, GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, GL_ARB_fragment_shader, GL_ARB_multisample, GL_ARB_occlusion_query, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shader_objects, GL_ARB_shading_language_100, GL_ARB_shadow, GL_ARB_shadow_ambient, GL_ARB_texture_border_clamp, GL_ARB_texture_compression, 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_float, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_rectangle, GL_ARB_transpose_matrix, GL_ARB_vertex_blend, GL_ARB_vertex_buffer_object, GL_ARB_pixel_buffer_object, GL_ARB_vertex_program, GL_ARB_vertex_shader, GL_ARB_window_pos, GL_ARB_draw_buffers, GL_ATI_draw_buffers, GL_ATI_element_array, GL_ATI_envmap_bumpmap, GL_ATI_fragment_shader, GL_ATI_map_object_buffer, GL_ATI_separate_stencil, GL_ATI_shader_texture_lod, GL_ATI_texture_compression_3dc, GL_ATI_texture_env_combine3, GL_ATI_texture_float, GL_ATI_texture_mirror_once, GL_ATI_vertex_array_object, GL_ATI_vertex_attrib_array_object, GL_ATI_vertex_streams, GL_ATIX_texture_env_combine3, GL_ATIX_texture_env_route, GL_ATIX_vertex_shader_output_point_size, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint, 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_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_wrap, GL_EXT_texgen_reflection, GL_EXT_texture3D, GL_EXT_texture_compression_s3tc, GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, GL_EXT_texture_rectangle, GL_EXT_vertex_array, GL_EXT_vertex_shader, GL_HP_occlusion_test, GL_NV_blend_square, GL_NV_occlusion_query, GL_NV_texgen_reflection, GL_SGI_color_matrix, GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod, 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 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x24 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x25 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x26 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x27 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x28 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x29 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x2a 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x2b 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x2c 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x2d 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x2e 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x2f 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x30 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x31 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x32 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x33 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x34 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x35 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x36 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x37 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x38 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x39 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x3a 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x3b 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x3c 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x3d 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x3e 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x3f 24 tc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x40 24 tc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x41 24 tc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x42 24 tc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x43 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x44 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x45 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x46 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x47 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x48 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x49 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x4a 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x4b 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x4c 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x4d 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x4e 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x4f 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x50 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x51 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x52 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x53 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x54 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x55 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x56 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x57 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x58 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x59 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x5a 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x5b 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x5c 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 16 16 16 16 0 0 None 0x5d 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x5e 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 16 16 16 16 0 0 None 0x5f 24 dc 0 32 0 r y . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x60 24 dc 0 32 0 r . . 8 8 8 8 0 24 8 0 0 0 0 0 0 None 0x61 24 dc 0 32 0 r y . 8 8 8 8 0 24 0 0 0 0 0 0 0 None 0x62 24 dc 0 32 0 r . . 8 8 8 8 0 24 0 0 0 0 0 0 0 None