Freesurfer March 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
79 discussions

preproc inorm question
by Cameron Ellis 02 Mar '07

02 Mar '07

Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did not want to smooth in the volume, would I need to preprocess my data again without smoothing or could I just specify the motion corrected volume in in a new analysis. I think the answer is: I could just specify the motion corrected volume, however, since the global mean for intensity normalization is calculated at the end of preprocessing after smoothing and exists in the fmcsm.meanval file, will there be a problem with the inorm in later stages, will it be performed etc. if I just specify the fmc volume in a new analysis? Thanks, Cameron

2 3

tksurfer window too small
by Joongnam Yang 02 Mar '07

02 Mar '07

Hi all, When I displayed a flattened image of the entire cortex (lh.full.patch.flat) on the tksurfer window, the image was too big for the tksurfer window, meaning the falttened image is chopped out. Is there any way that I can display the entire flattened image on the tksurfer window? Thanks. Nam.

2 1

longitudinal processing
by ccongle＠nmr.mgh.harvard.edu 02 Mar '07

02 Mar '07

Hi, I'm working with the recon-all -long processing stream. It went all the way through on one of my brains yesterday, but today it's stopping around here: ____________________________________________ invert the first LTA before applying it Talairach xfrm src file is /space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgz Talairach xfrm dst file is /usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305.mnc INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (172, 220, 156) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : ( 1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 1.0000, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.0950, -16.5100, 9.7500) file : /usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305.mnc volume geometry: extent : (86, 110, 68) voxel : ( 2.0000, 2.0000, 2.0000) x_(ras) : ( 1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 1.0000, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.0950, -16.5100, 9.7500) file : /usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 7.4766, 9.4936, -0.2721) file : /space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgzvolume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 7.4766, 9.4936, -0.2721) file : /space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgzRead individual LTAs Warning: dst volume of lta1 doesn't match src volume of lta2 Volume geometry for lta1-dst: Volume geometry for lta2-src: Combine the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2 xfma: Undefined variable. jizo:ccongle[116] _________________________________________________________ I'm not sure what the 'xfma' is. Do you know what the problem might be? Thanks, Christina

1 0

longitudinal processing
by ccongle＠nmr.mgh.harvard.edu 01 Mar '07

01 Mar '07

Hello, I'm trying to run the longitudinal processing pipeline, but can't figure out a command that works. Below is what I've tried and what has happened (MC-07M_prereconEDIT is the 'pre' timepoint, and MC-07M_post is the 'post'). Can you help? In dev env: jizo:ccongle[103] recon-all-long -long -tp1 MC-07M_prereconEDIT -s MC-07M_post recon-all-long: Command not found. jizo:ccongle[104] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post INFO: SUBJECTS_DIR is /autofs/space/jizo_001/users/STRUCTURALS/MBSR Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev ERROR: nothing to do In stable env: jizo:ccongle[85] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post ERROR: Flag -long unrecognized. -long -tp1 MC-07M_prereconEDIT -s MC-07M_post jizo:ccongle[87] recon-all-long -tp1 MC-07M_prereconEDIT -s MC-07M_post recon-all-long: Command not found. Thanks, Christina

2 1

tkmedit after mri convert
by Lindsay Casmaer 01 Mar '07

01 Mar '07

I am attempting to view the mgz files after converting from ima to mgz successfully. After attempting the command I get this error: tkmedit -f ${SUBJECTS_DIR}/030217_vc11174/mri/orig/001.mgz GLUT: Fatal Error in tkmedit.bin: could not open display: Any suggestions would be helpful. Thank you. Lindsay Casmaer

3 5

can not see surfaces
by Burak Ozkalayci 01 Mar '07

01 Mar '07

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

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annotations & functional activation
by oxro03＠yahoo.com 01 Mar '07

01 Mar '07

Hi Freesurfers, I have functional activation files (.mgh) which I can overlay onto a subject's surface. Now I am trying to do a functional ROI analysis based on the annotation files, e.g. to get information about the mean activation in a specific area based on FS segmentations. Does anybody have any suggestion on how to do this in a straightforward manner? Thanks a lot. Sandy --------------------------------- Any questions? Get answers on any topic at Yahoo! Answers. Try it now.

2 2

bus error during group analysis
by Leonardo Bonilha 28 Feb '07

28 Feb '07

Hi, I am getting a bus error during a group analysis and I wondered if someone could give me some help. I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8). While going through the steps from the web tutorial (with my own data) I am getting the following message: After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface /Applications/freesurfer//sub_aging//average/surf/lh.white reading group avg surface area 782 cm^2 from file Reading in average area /Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868 $Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47 greve Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error Interestingly, I ran the same analysis (with the same data) on another machine (this time a PC running Ubuntu) and it went fine, without any problems. Thanks for the support Leo Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication Sciences and Disorders University of South Carolina ____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/

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%GM, %WM, %CSF wrt ICV - including cerebellum
by Juranek, Jenifer 28 Feb '07

28 Feb '07

I'd like to compute %GM, %WM, %CSF wrt ICV (eTIV)...including cerebellum gray/white. Are the values returned by mris_wm_volume and mris_volume for cortical surfaces only (excluding cerebellum)? So, in this case... 1) are the values in aseg.stats appropriate for both cerebral and cerebellar fractions? 2) should a combination of cortical GM & WM from mris_volume be added to the cerebellar gm & wm values reported in aseg.stats to get TOTAL_GM and TOTAL_WM? 3) is it true that CSF= ICV - GM(cerebral and cerebellar) - WM(cerebral and cerebellar) Any advice is greatly appreciated... Many Thanks, Jenifer Juranek

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Freesurfer March 2007