Dear Freesurfer Experts, I have ran recon-all on a T1 SPGR image of a control subject without error. The outputs look reasonable (visually). However, the numbers I got from aseg.stats do not make sense (they are way off). Any thoughts?
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject AH --surf-wm-vol --ctab /mrbin/freesurfer.cver/ASegStatsLUT.txt # sysname Linux # machine x86_64 # anatomy_type volume # # SUBJECTS_DIR /freesurfer.v4.50/subjects # subjectname CTRL # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2009/12/28 13:45:15 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1403481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1403481.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1021869.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1034494, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1034494.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1218358.332484, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2009/12/28 20:51:43 # ColorTable /freesurfer.cver/ASegStatsLUT.txt # ColorTableTimeStamp 2009/08/11 08:24:37 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2009/12/28 14:25:34 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2009/12/28 14:25:34 # surface-based-volume mm3 lh-cerebral-white-matter 192622.906250 # surface-based-volume mm3 rh-cerebral-white-matter 198347.390625 # surface-based-volume mm3 tot-cerebral-white-matter 390970.296875 # ExcludeSegId 0 # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 49 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2 187032 187032.0 Left-Cerebral-White-Matter 102.5864 7.8948 42.0000 128.0000 86.0000 2 3 216661 216661.0 Left-Cerebral-Cortex 75.4785 9.6262 20.0000 120.0000 100.0000 3 4 5897 5897.0 Left-Lateral-Ventricle 46.5982 12.1178 21.0000 103.0000 82.0000 4 5 111 111.0 Left-Inf-Lat-Vent 53.2529 9.1730 31.0000 75.0000 44.0000 5 7 18124 18124.0 Left-Cerebellum-White-Matter 86.7241 5.8041 34.0000 108.0000 74.0000 6 8 48971 48971.0 Left-Cerebellum-Cortex 67.2554 9.0672 20.0000 94.0000 74.0000 7 10 5893 5893.0 Left-Thalamus-Proper 94.6949 7.5163 51.0000 115.0000 64.0000 8 11 2861 2861.0 Left-Caudate 89.1393 6.8791 54.0000 112.0000 58.0000 9 12 4485 4485.0 Left-Putamen 92.3673 5.6768 59.0000 107.0000 48.0000 10 13 1403 1403.0 Left-Pallidum 99.4880 9.0969 38.0000 117.0000 79.0000 11 14 848 848.0 3rd-Ventricle 53.1839 14.1313 9.0000 88.0000 79.0000 12 15 1595 1595.0 4th-Ventricle 43.9798 10.9321 19.0000 84.0000 65.0000 13 16 20022 20022.0 Brain-Stem 87.3585 9.3424 0.0000 111.0000 111.0000 14 17 3923 3923.0 Left-Hippocampus 79.3928 7.2511 47.0000 105.0000 58.0000 15 18 1332 1332.0 Left-Amygdala 75.6713 6.1980 53.0000 93.0000 40.0000 16 24 1112 1112.0 CSF 61.4318 13.1568 10.0000 115.0000 105.0000 17 26 603 603.0 Left-Accumbens-area 85.5804 4.0438 71.0000 102.0000 31.0000 18 28 3514 3514.0 Left-VentralDC 96.1436 8.7264 52.0000 112.0000 60.0000 19 30 42 42.0 Left-vessel 74.2500 7.1572 60.0000 87.0000 27.0000 20 31 1041 1041.0 Left-choroid-plexus 60.1743 12.6617 30.0000 94.0000 64.0000 21 41 193652 193652.0 Right-Cerebral-White-Matter 102.1858 8.4199 29.0000 128.0000 99.0000 22 42 218080 218080.0 Right-Cerebral-Cortex 74.1964 9.5593 24.0000 112.0000 88.0000 23 43 7313 7313.0 Right-Lateral-Ventricle 45.4438 12.3664 21.0000 96.0000 75.0000 24 44 186 186.0 Right-Inf-Lat-Vent 55.9329 9.9081 29.0000 80.0000 51.0000 25 46 17040 17040.0 Right-Cerebellum-White-Matter 89.3756 5.6165 41.0000 108.0000 67.0000 26 47 50180 50180.0 Right-Cerebellum-Cortex 68.7090 9.1593 15.0000 95.0000 80.0000 27 49 5702 5702.0 Right-Thalamus-Proper 94.7338 7.4958 52.0000 113.0000 61.0000 28 50 2742 2742.0 Right-Caudate 86.3893 7.4517 49.0000 109.0000 60.0000 29 51 4351 4351.0 Right-Putamen 92.2726 5.7435 62.0000 114.0000 52.0000 30 52 1267 1267.0 Right-Pallidum 99.1728 9.1982 47.0000 117.0000 70.0000 31 53 3650 3650.0 Right-Hippocampus 79.5501 7.5132 50.0000 109.0000 59.0000 32 54 1420 1420.0 Right-Amygdala 76.6007 5.3777 46.0000 94.0000 48.0000 33 58 618 618.0 Right-Accumbens-area 87.6877 5.1789 69.0000 108.0000 39.0000 34 60 3270 3270.0 Right-VentralDC 95.6004 10.3447 49.0000 114.0000 65.0000 35 62 40 40.0 Right-vessel 71.4286 7.5935 51.0000 86.0000 35.0000 36 63 857 857.0 Right-choroid-plexus 61.1068 11.6978 30.0000 89.0000 59.0000 37 72 58 58.0 5th-Ventricle 68.8148 9.9054 53.0000 97.0000 44.0000 38 77 2823 2823.0 WM-hypointensities 79.6001 12.5822 30.0000 106.0000 76.0000 39 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 40 79 0 0.0 Right-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 41 80 82 82.0 non-WM-hypointensities 65.6207 16.5103 29.0000 96.0000 67.0000 42 81 0 0.0 Left-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 43 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 44 85 188 188.0 Optic-Chiasm 76.3684 13.4378 46.0000 100.0000 54.0000 45 251 797 797.0 CC_Posterior 111.4135 8.5269 77.0000 123.0000 46.0000 46 252 344 344.0 CC_Mid_Posterior 102.7219 11.1890 60.0000 118.0000 58.0000 47 253 358 358.0 CC_Central 103.9541 9.0602 69.0000 114.0000 45.0000 48 254 366 366.0 CC_Mid_Anterior 104.4078 9.1388 77.0000 120.0000 43.0000 49 255 629 629.0 CC_Anterior 107.1212 9.0856 60.0000 122.0000 62.0000
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