hmmm, not sure about the tksurfer errors, but try not running tkmedit in the background (take the & out)
sounds like you have either a version mismatch or a tcl problem, but I'll leave it for Nick or Krish.
cheers, Bruce On Fri, 22 May 2009, Mayuresh Korgaonkar wrote:
Dear Freesurfer authors and users,
I recently installed the CentOS 4*86_64 Freesurfer v4.3.0 on a RedHat machine. After following each installation step, I have reached the testingFreesurfer module. However I seem to be having problems in running the first few steps. On running the "tkmedit bert orig.mgz" & "tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt" commands, all I get is "Setting subject to bert" and nothing happens following that.
Now, when I run the "tksurfer bert rh pial" I get errors (see at end of email). Any ideas whats going on and how I could fix this?
Thanks, Mayuresh
*********** error ****************
[root@localhost ~]# tksurfer bert rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /root surfer: all rgb files written to /root surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1..mgz surfer: vertices=131860, faces=263716 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) Tk_Init failed: this isn't a Tk applicationunknown color name "Black" Tix_Init failed: this isn't a Tk applicationunknown color name "Black" 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 Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl: this isn't a Tk applicationunknown color name "Black" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_InflatedVSetLoaded 0: can't read "glEnableGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0: can't read "glEnableGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded 0: can't read "glEnableGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0: can't read "glEnableGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0: can't read "glEnableGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0: can't read "glEnableGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0: can't read "glEnableGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0: can't read "glEnableGroups(mg_FieldMaskLoaded)": no such variable surfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OriginalVSetLoaded 1: can't read "glEnableGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command LblLst_SetStructures { 0 Unknown 1 G_cingularis 2 G_cuneus 3 G_frontalis_inf-pars_opercularis 4 G_frontalis_inf-pars_orbitalis 5 G_frontalis_inf-pars_triangularis 6 G_frontalis_medius 7 G_frontalis_sup-pars_lateralis 8 G_frontalis_sup-pars_medialis 9 G_frontomarginalis 10 G_hippocampi 11 G_insularis_breves 12 G_occipitalis_inf 13 G_occipitalis_medius-pars_inf 14 G_occipitalis_medius-pars_sup 15 G_occipitalis_sup 16 G_lateralis 17 G_lingualis 18 G_parahippocampi 19 G_orbitalis 20 G_paracentralis 21 G_parietalis_inf-pars_angularis 22 G_parietalis_inf-pars_supramarginalis 23 G_parietalis_sup 24 G_postcentralis 25 G_precentralis 26 G_precuneus 27 G_rectus_and_S_orbitalis_medialis 28 G_rectus_and_S_orbitalis_medialis2 29 G_subcentralis 30 G_supracingularis 31 G_temporalis_transversalis 32 G_temporalis_inf 33 G_temporalis_medius 34 G_temporalis_sup-pars_lateralis 35 G_temporalis_sup-planum_polare 36 G_temporalis_sup-planum_temporale 37 Plica_falciformis 38 Polus_occipitalis 39 Polus_temporalis 40 S_temporalis_transversalis 42 S_angularis 43 S_calcarinus 44 S_centralis_insulae_&_G_insularis_longus 46 S_centralis 47 S_cingularis 48 S_cingularis-pars_marginalis 49 S_circularis_insulae_ant 50 S_circularis_insulae_inf 51 S_circularis_insulae_sup 52 S_corpori_callosi 53 S_diagonalis 54 S_frontalis_inf 55 S_frontalis_medialis 56 S_frontalis_medius 57 S_frontalis_sup 58 S_frontomarginalis 59 S_intermedius_primus 60 S_intermedius_secundus 61 S_intracingularis 62 S_intraoccipitalis_medius 63 S_intraoccipitotemporalis_lateralis 64 S_intraparietalis 65 S_lateralis-pars_ant-ramus_horizontalis 66 S_lateralis-pars_ant-ramus_verticalis 67 S_lateralis-pars_horizontalis 68 S_lateralis-pars_post 69 S_lunatus 70 S_occipitalis_ant 71 S_occipitalis_inf 72 S_occipitalis_medius 73 S_occipitalis_sup 74 S_occipitalis_transversalis 75 S_occipitopolaris 76 S_occipitotemporalis_lateralis 77 S_occipitotemporalis_medialis 78 S_orbitales 79 S_orbitalis_lateralis 80 S_paracalcarinus 81 S_paracentralis 82 S_parietalis_transversalis 83 S_parieto_occipitalis 84 S_postcentralis 85 S_precentralis 86 S_retrocalcarinus 87 S_rhinalis 88 S_subcentralis_ant_&_post_ 89 S_suborbitalis 90 S_subparietalis 91 S_supracingularis 92 S_temporalis_inf 93 S_temporalis_sup 94 S_triangularis }: invalid command name "LblLst_SetStructures" reading white matter vertex locations... surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_WhiteVSetLoaded 1: can't read "glEnableGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command UpdateLinkedVarGroup all: invalid command name "UpdateLinkedVarGroup" % surfer: Error sending tcl command MoveToolWindow 663 681: invalid command name "MoveToolWindow"
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