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 **********************************************
Hi, I just ran mri_aparc2aseg on a group of subjects, and a couple of them failed to produce an output file despite lacking any apparent error messages. The command I ran was (with subj name replaced):
mri_aparc2aseg --s ###### --o aparc_cor+aseg.mgz --ribbon --annot final
These are subjects whose aparcs have been edited, but still have only the standard set of labels. The screen output for one that failed was:
SUBJECTS_DIR /j/rstruc2/surfaces/sibstudy/nc subject ###### outvol aparc_cor+aseg.mgz useribbon 1 baseoffset 0
Reading lh white surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/lh.white
Building hash of lh white
Reading lh pial surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/lh.pial
Building hash of lh pial
Loading lh annotations from /j/rstruc2/surfaces/sibstudy/nc/######/label/lh.final.annot reading colortable from annotation file... colortable with 35 entries read (originally /autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortable_final.txt)
Reading rh white surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/rh.white
Building hash of rh white
Reading rh pial surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/rh.pial
Building hash of rh pial
Loading rh annotations from /j/rstruc2/surfaces/sibstudy/nc/######/label/rh.final.annot reading colortable from annotation file... colortable with 35 entries read (originally /autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortable_final.txt) Have color table for lh white annotation Have color table for rh white annotation Loading lh ribbon mask from /j/rstruc2/surfaces/sibstudy/nc/######/mri/lh.ribbon.mgz Talairach transform /data1/c/brad/subjects/surfaces/######/mri/transforms/talairach.xfm does not exist... Loading tal xfm file /j/rstruc2/surfaces/sibstudy/nc/######/mri/transforms/talairach.xfm Loading rh ribbon mask from /j/rstruc2/surfaces/sibstudy/nc/######/mri/rh.ribbon.mgz Talairach transform /data1/c/brad/subjects/surfaces/######/mri/transforms/talairach.xfm does not exist... Loading tal xfm file /j/rstruc2/surfaces/sibstudy/nc/######/mri/transforms/talairach.xfm
Loading aseg from /j/rstruc2/surfaces/sibstudy/nc/######/mri/aseg.mgz Talairach transform /data1/c/brad/subjects/surfaces/######/mri/transforms/talairach.xfm does not exist... Loading tal xfm file /j/rstruc2/surfaces/sibstudy/nc/######/mri/transforms/talairach.xfm ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -------------------------
Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 aseg id = 3 crs = 142 142 158, ras = -14.0000 30.0000 -14.0000 lhw 122604 2.06939 -15.8773 30.8370 -14.2401 lhp 122604 0.63675 -13.6225 29.9035 -14.5036 rhp 122694 13.50887 -0.9827 29.1451 -10.4915 annot = 0, annotid = -1 0 unknown 25 5 25 0 1 bankssts 25 100 40 0 2 caudalanteriorcingulate 125 100 160 0 3 caudalmiddlefrontal 100 25 0 0 4 corpuscallosum 120 70 50 0 5 cuneus 220 20 100 0 6 entorhinal 220 20 10 0 7 fusiform 180 220 140 0 8 inferiorparietal 220 60 220 0 9 inferiortemporal 180 40 120 0 10 isthmuscingulate 140 20 140 0 11 lateraloccipital 20 30 140 0 12 lateralorbitofrontal 35 75 50 0 13 lingual 225 140 140 0 14 medialorbitofrontal 200 35 75 0 15 middletemporal 160 100 50 0 16 parahippocampal 20 220 60 0 17 paracentral 60 220 60 0 18 parsopercularis 220 180 140 0 19 parsorbitalis 20 100 50 0 20 parstriangularis 220 60 20 0 21 pericalcarine 120 100 60 0 22 postcentral 220 20 20 0 23 posteriorcingulate 220 180 220 0 24 precentral 60 20 220 0 25 precuneus 160 140 180 0 26 rostralanteriorcingulate 80 20 140 0 27 rostralmiddlefrontal 75 50 125 0 28 superiorfrontal 20 220 160 0 29 superiorparietal 20 180 140 0 30 superiortemporal 140 220 220 0 31 supramarginal 80 160 20 0 32 frontalpole 100 0 100 0 33 temporalpole 70 70 70 0 34 transversetemporal 150 150 200 0
I also tried setting the output to save in my home directory, so I'm certain the problem isn't that it doesn't have permission to write the file, and the majority of subjects did not have this problem. Does anyone have any idea why this might be happening (or what other information would be needed to determine the problem)?
Thanks,
-Aaron-
Okay, never mind. It turned out there were a couple nodes without labels that'd been screwing things up.
Thanks,
-Aaron-
-----Original Message----- From: Goldman, Aaron (NIH/NIMH) [C] Sent: Monday, May 14, 2007 4:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Failure of mri_aparc2aseg
Hi, I just ran mri_aparc2aseg on a group of subjects, and a couple of them failed to produce an output file despite lacking any apparent error messages. The command I ran was (with subj name replaced):
mri_aparc2aseg --s ###### --o aparc_cor+aseg.mgz --ribbon --annot final
These are subjects whose aparcs have been edited, but still have only the standard set of labels. The screen output for one that failed was:
SUBJECTS_DIR /j/rstruc2/surfaces/sibstudy/nc subject ###### outvol aparc_cor+aseg.mgz useribbon 1 baseoffset 0
Reading lh white surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/lh.white
Building hash of lh white
Reading lh pial surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/lh.pial
Building hash of lh pial
Loading lh annotations from /j/rstruc2/surfaces/sibstudy/nc/######/label/lh.final.annot reading colortable from annotation file... colortable with 35 entries read (originally /autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortab le_final.txt)
Reading rh white surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/rh.white
Building hash of rh white
Reading rh pial surface /j/rstruc2/surfaces/sibstudy/nc/######/surf/rh.pial
Building hash of rh pial
Loading rh annotations from /j/rstruc2/surfaces/sibstudy/nc/######/label/rh.final.annot reading colortable from annotation file... colortable with 35 entries read (originally /autofs/space/birn_044/users/buckner_surf_atlas_rebuild/scripts/colortab le_final.txt) Have color table for lh white annotation Have color table for rh white annotation Loading lh ribbon mask from /j/rstruc2/surfaces/sibstudy/nc/######/mri/lh.ribbon.mgz Talairach transform /data1/c/brad/subjects/surfaces/######/mri/transforms/talairach.xfm does not exist... Loading tal xfm file /j/rstruc2/surfaces/sibstudy/nc/######/mri/transforms/talairach.xfm Loading rh ribbon mask from /j/rstruc2/surfaces/sibstudy/nc/######/mri/rh.ribbon.mgz Talairach transform /data1/c/brad/subjects/surfaces/######/mri/transforms/talairach.xfm does not exist... Loading tal xfm file /j/rstruc2/surfaces/sibstudy/nc/######/mri/transforms/talairach.xfm
Loading aseg from /j/rstruc2/surfaces/sibstudy/nc/######/mri/aseg.mgz Talairach transform /data1/c/brad/subjects/surfaces/######/mri/transforms/talairach.xfm does not exist... Loading tal xfm file /j/rstruc2/surfaces/sibstudy/nc/######/mri/transforms/talairach.xfm ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -------------------------
Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 aseg id = 3 crs = 142 142 158, ras = -14.0000 30.0000 -14.0000 lhw 122604 2.06939 -15.8773 30.8370 -14.2401 lhp 122604 0.63675 -13.6225 29.9035 -14.5036 rhp 122694 13.50887 -0.9827 29.1451 -10.4915 annot = 0, annotid = -1 0 unknown 25 5 25 0 1 bankssts 25 100 40 0 2 caudalanteriorcingulate 125 100 160 0 3 caudalmiddlefrontal 100 25 0 0 4 corpuscallosum 120 70 50 0 5 cuneus 220 20 100 0 6 entorhinal 220 20 10 0 7 fusiform 180 220 140 0 8 inferiorparietal 220 60 220 0 9 inferiortemporal 180 40 120 0 10 isthmuscingulate 140 20 140 0 11 lateraloccipital 20 30 140 0 12 lateralorbitofrontal 35 75 50 0 13 lingual 225 140 140 0 14 medialorbitofrontal 200 35 75 0 15 middletemporal 160 100 50 0 16 parahippocampal 20 220 60 0 17 paracentral 60 220 60 0 18 parsopercularis 220 180 140 0 19 parsorbitalis 20 100 50 0 20 parstriangularis 220 60 20 0 21 pericalcarine 120 100 60 0 22 postcentral 220 20 20 0 23 posteriorcingulate 220 180 220 0 24 precentral 60 20 220 0 25 precuneus 160 140 180 0 26 rostralanteriorcingulate 80 20 140 0 27 rostralmiddlefrontal 75 50 125 0 28 superiorfrontal 20 220 160 0 29 superiorparietal 20 180 140 0 30 superiortemporal 140 220 220 0 31 supramarginal 80 160 20 0 32 frontalpole 100 0 100 0 33 temporalpole 70 70 70 0 34 transversetemporal 150 150 200 0
I also tried setting the output to save in my home directory, so I'm certain the problem isn't that it doesn't have permission to write the file, and the majority of subjects did not have this problem. Does anyone have any idea why this might be happening (or what other information would be needed to determine the problem)?
Thanks,
-Aaron-
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Goldman, Aaron (NIH/NIMH) [C] -
Lee, Jung Min