Does the aseg look correct? If so, how about the aparc+aseg? On Wed, 30 Dec 2009, Hui J Yu wrote:
> 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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
