Re: [Freesurfer] can not see surfaces
Thanks for your attention however I am using ATI Mobility Radeon X1400 graphics card and just installed the drivers. They must be up to date. ??? Burak Nick Schmansky wrote: Burak, If you are using an NVidia graphics card, then you will need to upgrade the driver to the newest version (goto the nvidia site to do this). This problem, of displaying a sliver in tksurfer, has been seen before, and upgrading the driver will fix it. Nick On Thu, 2007-03-01 at 17:10 +0100, Burak Ozkalayci wrote: 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 [EMAIL PROTECTED] 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 -- [EMAIL PROTECTED] 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_ver
[Freesurfer] volume index vertex positions
Hi surfers, Last time I asked how to see and access to the thickness values and your advices worked. Thanks a lot. When I checked the asci file, which I acquired by converting the thickness file, I saw that the X Y Z coordinates of the vertices are given in talairach coordinates. However I need them in volume index coordinate. Is it possible? Thanks in advance. Burak ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Grainy thickness ribbon
Dear surfers, I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon it generates a very grainy map. I think that those unassigned voxels are not hit by the normals of vertices on the white surface. To compensate it I tried to fill the ribon with the normals originated from the pial surface by : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial however the ribbon I get is shifted to the outer side of the cortex. I think the normals of the pial are oriented to show outer space of the cortex and they hit the voxels at the outerspace. I also attached the thickness maps of the ribbon I get from the white and the pial surfaces and the T1 image. They are the same slice of the volume, and you can see that pial one passes beyond the pial surface in general. In the help of mri_surf2vol for the fillribbon option, it is explained as "iterate projfrac from 0 to 1". And when the code is running I saw that iteration has a 0.05 step. I wonder whether is it possible to define the stepsize and the range for example 0 to -1 to reverse the hitting voxels. Thanks in advance. Burak thicknessRibbon.tar.gz Description: GNU Zip compressed data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] vertex normals
Hi all, I want to get an ascii file listing the normal vectors of each vertex of the surface (white or pial). In http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02210.html mri_surf2surf is adviced to used but I could not find any example usage for creating vertex normals. And I appreciate any help on converting the output of the mri_surf2surf to ascii file. One more question about the vertex normals. using tksurfer to see the surfaces, the normals of the selected vertices are printed on the console. to use mri_surf2surf the sphere.reg files are needed and they are created at the 3rd step of reconall. If there is any straightway to get those vertex normals from the surface definition like tksurfer do, I prefer it since I do not want to wait for the reconall 3. Thanks in advance. Burak ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] vertex normals
Nick, Thanks a lot. That is just what I am looking for, and it is working perfect. Burak Nick Schmansky wrote: Burak, I've update mris_convert so that it outputs the normal vectors of each vertex of the surface. You can get this binary for Linux here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist Copy the file mris_convert.gz to your $FREESURFER_HOME/bin, then type: gunzip mris_convert.gz chmod a+x mris_convert Then type 'mris_convert' for help. The new flag is '-n', so example usage is: mris_convert -n lh.white lh.white.normals.asc Recall that: mris_convert lh.white lh.white.asc will give you the file lh.white.asc containing the xyz of each vertex (plus face info), so of course this file is paired with lh.white.normals.asc (the difference being that this file has the normal vectors for each vertex). Hope this is what you needed. Nick On Fri, 2007-05-04 at 18:46 +0200, burak ozkalayci wrote: Hi all, I want to get an ascii file listing the normal vectors of each vertex of the surface (white or pial). In http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02210.html mri_surf2surf is adviced to used but I could not find any example usage for creating vertex normals. And I appreciate any help on converting the output of the mri_surf2surf to ascii file. One more question about the vertex normals. using tksurfer to see the surfaces, the normals of the selected vertices are printed on the console. to use mri_surf2surf the sphere.reg files are needed and they are created at the 3rd step of reconall. If there is any straightway to get those vertex normals from the surface definition like tksurfer do, I prefer it since I do not want to wait for the reconall 3. Thanks in advance. Burak ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer begin:vcard fn:Burak Ozkalayci n:Ozkalayci;Burak org:Ghent University Hospital - IBITECH;Electronic and Information Systems (ELIS-MEDISIP) adr:De Pintelaan 185;;Block B - IBITECH - 514;Gent;;9000;Belgium email;internet:[EMAIL PROTECTED] title:PhD Student version:2.1 end:vcard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] About tissue probability maps from aseg.mgz
Dear surfers, I want to ask whether it is possible to have a tissue probability map of the brain according to aseg.mgz. If I am not wrong aseg.mgz is the MAP estimate of a Markov Random Field based segmentation hence we shall get the probability maps for each label or tissue. Is it possible? Best, Burak begin:vcard fn:Burak Ozkalayci n:Ozkalayci;Burak org:Ghent University Hospital - IBITECH;Electronic and Information Systems (ELIS-MEDISIP) adr:De Pintelaan 185;;Block B - IBITECH - 514;Gent;;9000;Belgium email;internet:[EMAIL PROTECTED] title:PhD Student version:2.1 end:vcard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
