Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

63 participants
95 discussions

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.

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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,

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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. 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

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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

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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

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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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extracting BA6
by Behrang Nosrat Makouei 28 May '08

28 May '08

Hi FreeSurfer Community, I was wondering if we can extract BA6 from aseg.mgz or aparc+aseg.mgz I noticed BA6 was added after ver 4.0.3 but when I tried "mri_extract_label aparc+aseg.mgz 406 output.mgz" or "mri_extract_label aseg.mgz 406 output.mgz" I get empty volumes for the output.mgz. Thanks, --------------------------------------------------- Behrang Nosrat Makouei Engineering Science PhD. Candidate Simon Fraser University, Burnaby, Canada TASC 9400 Tel: 778 885 5016 Email: bnosratm(a)sfu.ca

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tksurfer display broken: "smart" over-ride?
by Juranek, Jenifer 28 May '08

28 May '08

Krish & Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a "smart" window pops up reporting that "a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed". I select "OK" anyway, but a new window pops-up reporting that "No packages were given for installation". How do I over-ride the "smart" system to install the legacy driver I need to make sure that everything is installed in the proper place(s) to make tksurfer happy again? Thanks so much, Jenifer

2 3

QDEC and Slicer3
by Pedro Paulo de Magalhães Oliveira Junior 27 May '08

27 May '08

Hi, Installing Slicer3 yesterday I have noticed that it seems to have a QDEC module. Is there any documentation on this? Thanks Pedro Paulo Jr

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Freesurfer May 2008