Dear All,
We are making Volume-based analyses and I have a few questions.
1. The SupraTentorial BrainVolume is indicated in the aseg.stats. I found an explanation on http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats about the SupraTentorial Vol., but checking the formula by summing up Cortex + CorticalWhiteMatter + SubCortGray I do not arrive at the exact value of SupraTentorial as indicated in the aseg.stats; for some of my subjects this value is higher, for some lower. What could cause these differences except from differences between voxel-based measures (i.e., SubCortGray) and surface-based measures? Is CSF and ventricle volume already subtracted from this value?
Please see below copied the aseg.stats file for one subject: Cortex 448248.101786 + CorticalWhiteMatter 404368.03125 + SubCortGray 215645 = 1068261.13. This differs from the supratentorial value indicated in aseg.stats, which is 1218507.78.
2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? If there are any lesions in structures, I would like to subtract lesion volume these structures that are listed in aseg.stats.
Best Regards,
Ruthger Righart (PhD)
Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany
Ruthger.Righart@med.uni-muenchen.de
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /Applications/freesurfer/ASegStatsLUT.txt --subject 1008 # # SUBJECTS_DIR /Network/Xgrid/freesurfer_M0HL # subjectname 1008 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 225756.920309, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 222491.181478, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 448248.101786, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 198684.625000, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 205683.406250, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 404368.031250, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 215645.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 663893.101786, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1218507.775726, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1882094.762769, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2010/12/01 23:41:35 # ColorTable /Applications/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2010/08/15 20:35:08 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2010/12/01 18:52:15 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2010/12/01 18:52:15 # Excluding Cortical Gray and White Matter # ExcludeSegId 0 2 3 41 42 # 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 45 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 44165 44165.0 Left-Lateral-Ventricle 19.7155 16.3746 0.0000 89.0000 89.0000 2 5 2806 2806.0 Left-Inf-Lat-Vent 38.3263 15.7951 0.0000 83.0000 83.0000 3 7 13657 13657.0 Left-Cerebellum-White-Matter 81.6728 7.8804 19.0000 104.0000 85.0000 4 8 58247 58247.0 Left-Cerebellum-Cortex 66.2938 9.3009 14.0000 102.0000 88.0000 5 10 7895 7895.0 Left-Thalamus-Proper 85.7346 10.2295 28.0000 119.0000 91.0000 6 11 7039 7039.0 Left-Caudate 76.7953 9.8187 43.0000 106.0000 63.0000 7 12 9318 9318.0 Left-Putamen 80.9289 7.7446 46.0000 105.0000 59.0000 8 13 1860 1860.0 Left-Pallidum 101.4026 7.2644 68.0000 125.0000 57.0000 9 14 3552 3552.0 3rd-Ventricle 32.3747 10.6085 7.0000 78.0000 71.0000 10 15 5173 5173.0 4th-Ventricle 26.7739 9.2009 5.0000 69.0000 64.0000 11 16 21267 21267.0 Brain-Stem 80.5809 11.2668 0.0000 112.0000 112.0000 12 17 4285 4285.0 Left-Hippocampus 71.2247 8.9495 37.0000 103.0000 66.0000 13 18 2061 2061.0 Left-Amygdala 70.0988 7.7635 46.0000 95.0000 49.0000 14 24 2125 2125.0 CSF 45.0837 14.0328 0.0000 91.0000 91.0000 15 26 353 353.0 Left-Accumbens-area 74.6694 8.4345 36.0000 97.0000 61.0000 16 28 3929 3929.0 Left-VentralDC 91.5580 11.5144 25.0000 138.0000 113.0000 17 30 80 80.0 Left-vessel 69.7313 10.6466 44.0000 93.0000 49.0000 18 31 3060 3060.0 Left-choroid-plexus 53.4769 14.2466 16.0000 97.0000 81.0000 19 43 41682 41682.0 Right-Lateral-Ventricle 20.2051 17.6097 0.0000 95.0000 95.0000 20 44 2696 2696.0 Right-Inf-Lat-Vent 35.8659 13.8272 5.0000 82.0000 77.0000 21 46 13037 13037.0 Right-Cerebellum-White-Matter 78.5698 7.4065 15.0000 101.0000 86.0000 22 47 63878 63878.0 Right-Cerebellum-Cortex 62.0222 8.9751 9.0000 114.0000 105.0000 23 49 8346 8346.0 Right-Thalamus-Proper 82.2752 10.6945 17.0000 117.0000 100.0000 24 50 6893 6893.0 Right-Caudate 77.8693 10.4023 40.0000 107.0000 67.0000 25 51 7934 7934.0 Right-Putamen 82.6062 7.5576 35.0000 109.0000 74.0000 26 52 1465 1465.0 Right-Pallidum 99.2448 8.3569 66.0000 125.0000 59.0000 27 53 4524 4524.0 Right-Hippocampus 69.3366 8.3325 41.0000 100.0000 59.0000 28 54 2064 2064.0 Right-Amygdala 70.9995 7.2951 46.0000 94.0000 48.0000 29 58 495 495.0 Right-Accumbens-area 82.1215 7.6559 53.0000 102.0000 49.0000 30 60 3792 3792.0 Right-VentralDC 91.5163 11.6881 35.0000 139.0000 104.0000 31 62 60 60.0 Right-vessel 67.9400 12.2748 43.0000 95.0000 52.0000 32 63 2811 2811.0 Right-choroid-plexus 54.0732 12.8437 11.0000 105.0000 94.0000 33 72 2 2.0 5th-Ventricle 53.6667 15.3080 36.0000 63.0000 27.0000 34 77 76464 76464.0 WM-hypointensities 77.3176 11.2567 3.0000 116.0000 113.0000 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 36 79 0 0.0 Right-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 37 80 176 176.0 non-WM-hypointensities 67.8028 9.9931 39.0000 87.0000 48.0000 38 81 0 0.0 Left-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 39 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 40 85 279 279.0 Optic-Chiasm 74.4070 19.3980 32.0000 121.0000 89.0000 41 251 694 694.0 CC_Posterior 101.0552 12.4533 53.0000 129.0000 76.0000 42 252 314 314.0 CC_Mid_Posterior 100.2673 10.3702 63.0000 122.0000 59.0000 43 253 341 341.0 CC_Central 103.2910 10.9173 68.0000 125.0000 57.0000 44 254 354 354.0 CC_Mid_Anterior 105.7351 13.7075 66.0000 137.0000 71.0000 45 255 780 780.0 CC_Anterior 106.4097 12.6707 70.0000 132.0000 62.0000