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 $FREESURFER_HOME/FreeSurferColorLUT.txt" commands, all I get is
"Setting subject to bert" and nothing happens following that.
Now, when I run the "tksurfer bert rh pial" I get errors (see at end of email).
Any ideas whats going on and how I could fix this?
Thanks,
Mayuresh
*********** error ****************
[r...@localhost ~]# tksurfer bert rh pial
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($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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