Hi,
I was able to use surf-sess command (modified in our group) to take pictures (rgb) of the brain; however, several days ago, I was kept getting errors (even errors with commands that worked fine before). it keep saying tksurfer.new: Command not found., then quit. Would you help me out?
Machine: Roma /space/roma/1/users/caplan/plaus2 Env: Standard environment Subjects_Dir: /space/thor/1/users/west/subjects
[roma:plaus2] (nmr-std-env) /space/roma/1/users/caplan/plaus2/scripts/surf-sess-rgb_wfile \ ? -analysis plaus2_corr \ ? -space sph \ ? -spacedir sph20 \ ? -subject west_margaret \ ? -s isxavg-plaus2_corr \ ? -contrast implaus_plaus_8-12sum \ ? -map sig \ ? -fthresh 1.3 \ ? -fmid 2.0 \ ? -fslope 1 \ ? -df dir \ ? -isxavg random \ ? -avgcurv \ ? -offset 0 \ ? -wfile /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w \ ? -hemi lh \ ? -rgbname plaus2_corr_implaus_plaus_8-12sum_300 cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /dev/null -----------------------------------------------------------------
---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- INFO: You are about to use the NEW version of tksurfer. INFO: If you want to use the OLD version, re-run surf-sess INFO: with the -old flag. ---------->>>>>>>>>>>....<<<<<<<<<<<<--------------------
------------------------------------------------------ ------------------------------------------------------ Session: isxavg-plaus2_corr ---- ------ lh hemisphere ------ sig-0-west_margaret west_margaret nowsource west_margaret equal wfile is /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w ------------ tcl file ----------- set val /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w sclv_read_binary_values 0 set curv lh.avg_curv read_binary_curv; set curvflag 1; source /usr/local/freesurfer/stable/lib/tcl/readenv.tcl file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb open_window sclv_set_current_field 0 puts "Taking Snapshots..." make_lateral_view redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_lat.rgb save_rgb rotate_brain_x 90 redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_ven.rgb save_rgb make_lateral_view rotate_brain_y 180 redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_med.rgb save_rgb exit --------------------------------- ---------------------------------------------------------- /autofs/space/roma_001/users/caplan/plaus2/isxavg-plaus2_corr/bold/plaus2_corr/s ph20-rfx/implaus_plaus_8-12sum tksurfer.new -west_margaret lh inflated -tcl /tmp/surf-sess-22861.tcl ---------------------------------------------------------- tksurfer.new: Command not found. Mon May 14 12:43:08 EDT 2007
I am also attaching the /surf-sess-rgb_wfile under command line.
Thanks a lot! -Jung Min
********************************************** Jung Min Lee Neurology/Neuropsychology Martinos Center for Biomedical Imaging Massachusetts General Hospital Tel: 617-726-0303 (work) 617-780-1900 (cell) e-mail: jlee63@partners.org mailto:jlee63@partners.org jmlee@nmr.mgh.harvard.edu mailto:jmlee@nmr.mgh.harvard.edu **********************************************