Dear FS experts,

We have a situation where mri_aparc2seg is failing on some subjects but not others. Since the processing on all the subjects up to this step was the same, we’re trying to figure out the problem. We’re using version 3.05 on a linux system. Here is the log:

***************************** mri_aparc2aseg failing log *********************

mri_aparc2aseg --s 000981972381 --a2005s
SUBJECTS_DIR
subject /phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381
outvol //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/mri/aparc.a2005s+aseg.mgz
useribbon 0
baseoffset 100

Reading lh white surface
 //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/surf/lh.white

Building hash of lh white

Reading lh pial surface
 //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/surf/lh.pial
Building hash of lh pial

Loading lh annotations from //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/label/lh.aparc.a2005s.annot
reading colortable from annotation file...
colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt)

Reading rh white surface
 //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/surf/rh.white

Building hash of rh white

Reading rh pial surface
 //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/surf/rh.pial

Building hash of rh pial

Loading rh annotations from //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/label/rh.aparc.a2005s.annot
reading colortable from annotation file...
colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading aseg from //phase2data/phase2Prep/preproc/download2/uci/FreesurferAnalyses/000981972381/mri/aseg.mgz
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 ERROR: could not map to any surface.
crs = 121 137 152, ras = 7.0000 24.0000 -9.0000

what’s that indicate?

Many thanks,

Jess

------------------------

Jessica Turner, Ph.D.

Project Manager, FBIRN (www.nbirn.net)

Department of Psychiatry and Human Behavior

University of California, Irvine

Phone: (949) 824-3331

Fax: (949) 824-3324