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- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
