Why in the aseg.stats file the nvoxel value doesn't equal to the volume or follow a arithmetic correlation?
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Hi all. I was puzzled when I checked the the aseg.stats in the fs_output_folder after I run the routuine recon-all cmd.(fs6.0_linux) In this stat file I found that the nvoxel value doesn't equal to the volumes of each subcortical segmentation. They even doesn't follow a arithmetic correlation. But the header reads that the voxel is equal to 1 mm^3 in volume. So why? I wiil be greatly appreciated if somebody could tell me if there is anything wrong with my ideas.
the sample of my aseg.stat file(some lines) is appended here.
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # VoxelVolume_mm3 1 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 18001 18343.9 Left-Lateral-Ventricle 37.8841 9.3238 24.0000 90.0000 66.0000 2 5 1641 1672.0 Left-Inf-Lat-Vent 45.0488 11.6523 23.0000 82.0000 59.0000 3 7 16241 16825.4 Left-Cerebellum-White-Matter 84.3527 5.6642 29.0000 98.0000 69.0000 4 8 52760 52711.2 Left-Cerebellum-Cortex 66.2411 9.4589 25.0000 91.0000 66.0000 5 10 7246 6891.5 Left-Thalamus-Proper 91.3607 9.1942 41.0000 107.0000 66.0000 6 11 3246 3140.1 Left-Caudate 85.8783 7.9460 53.0000 107.0000 54.0000 7 12 4285 4264.4 Left-Putamen 91.0488 4.3328 63.0000 104.0000 41.0000 8 13 2022 2006.2 Left-Pallidum 100.0514 4.3088 75.0000 118.0000 43.0000 9 14 2969 3048.2 3rd-Ventricle 39.8787 8.2650 26.0000 81.0000 55.0000 10 15 1552 1705.4 4th-Ventricle 40.3808 9.6486 23.0000 79.0000 56.0000 11 16 19144 18890.9 Brain-Stem 83.6324 10.1835 34.0000 108.0000 74.0000 12 17 3738 3442.8 Left-Hippocampus 74.7269 8.1358 40.0000 97.0000 57.0000 13 18 1100 1054.6 Left-Amygdala 76.2536 7.1347 43.0000 95.0000 52.0000 14 24 1791 1694.4 CSF 51.9894 11.2187 32.0000 94.0000 62.0000 15 26 278 249.5 Left-Accumbens-area 85.4928 6.2711 54.0000 93.0000 39.0000 16 28 4171 3992.6 Left-VentralDC 92.5809 11.1675 41.0000 116.0000 75.0000 17 30 0 0.0 Left-vessel 0.0000 0.0000 0.0000 0.0000 0.0000 18 31 928 888.8 Left-choroid-plexus 52.3438 10.8472 31.0000 78.0000 47.0000 19 43 20737 20900.1 Right-Lateral-Ventricle 37.1717 8.9953 25.0000 92.0000 67.0000 20 44 5481 5495.9 Right-Inf-Lat-Vent 37.8816 9.1653 26.0000 79.0000 53.0000 21 46 16633 17143.0 Right-Cerebellum-White-Matter 83.6901 5.3551 40.0000 99.0000 59.0000 22 47 54353 54454.1 Right-Cerebellum-Cortex 66.2976 9.1862 20.0000 89.0000 69.0000 23 49 6416 6042.8 Right-Thalamus-Proper 89.1852 9.9130 37.0000 106.0000 69.0000 24 50 3294 3062.4 Right-Caudate 87.1703 8.2085 53.0000 107.0000 54.0000 25 51 3794 3796.8 Right-Putamen 92.5113 4.1020 62.0000 104.0000 42.0000 26 52 2124 2028.5 Right-Pallidum 102.1172 4.1392 75.0000 118.0000 43.0000 27 53 2980 2742.1 Right-Hippocampus 73.9638 9.4803 28.0000 96.0000 68.0000 28 54 1299 1132.8 Right-Amygdala 69.1655 14.6045 28.0000 98.0000 70.0000 29 58 273 223.8 Right-Accumbens-area 88.0403 5.5989 64.0000 99.0000 35.0000 30 60 3924 3713.0 Right-VentralDC 92.1210 12.3974 35.0000 117.0000 82.0000 31 62 13 24.5 Right-vessel 60.4615 6.2930 48.0000 71.0000 23.0000 32 63 1302 1224.4 Right-choroid-plexus 51.1751 10.0901 31.0000 79.0000 48.0000 33 72 0 0.0 5th-Ventricle 0.0000 0.0000 0.0000 0.0000 0.0000 34 77 1508 1452.2 WM-hypointensities 74.0351 13.0445 37.0000 107.0000 70.0000 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000
Thank you!
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Yongxiang Zhao Ph.D. student Radiology Department of Xuanwu Hospital, Capital Medical University
2014-2017 Xuanwu Hospital, Capital Medical University Postgraduate 2009-2014 Qingdao Medical College Undergraduate
Hi Yongxiang
we compute partial-volume corrected volumes by estimating the mixing fraction of every border voxel. This significantly increases reliability (and presumably accuracy)
cheers Bruce On Tue, 12 Feb 2019, 赵永翔 wrote:
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Hi all. I was puzzled when I checked the the aseg.stats in the fs_output_folder after I run the routuine recon-all cmd.(fs6.0_linux) In this stat file I found that the nvoxel value doesn't equal to the volumes of each subcortical segmentation. They even doesn't follow a arithmetic correlation. But the header reads that the voxel is equal to 1 mm^3 in volume. So why? I wiil be greatly appreciated if somebody could tell me if there is anything wrong with my ideas.
the sample of my aseg.stat file(some lines) is appended here.
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # VoxelVolume_mm3 1 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 18001 18343.9 Left-Lateral-Ventricle 37.8841 9.3238 24.0000 90.0000 66.0000 2 5 1641 1672.0 Left-Inf-Lat-Vent 45.0488 11.6523 23.0000 82.0000 59.0000 3 7 16241 16825.4 Left-Cerebellum-White-Matter 84.3527 5.6642 29.0000 98.0000 69.0000 4 8 52760 52711.2 Left-Cerebellum-Cortex 66.2411 9.4589 25.0000 91.0000 66.0000 5 10 7246 6891.5 Left-Thalamus-Proper 91.3607 9.1942 41.0000 107.0000 66.0000 6 11 3246 3140.1 Left-Caudate 85.8783 7.9460 53.0000 107.0000 54.0000 7 12 4285 4264.4 Left-Putamen 91.0488 4.3328 63.0000 104.0000 41.0000 8 13 2022 2006.2 Left-Pallidum 100.0514 4.3088 75.0000 118.0000 43.0000 9 14 2969 3048.2 3rd-Ventricle 39.8787 8.2650 26.0000 81.0000 55.0000 10 15 1552 1705.4 4th-Ventricle 40.3808 9.6486 23.0000 79.0000 56.0000 11 16 19144 18890.9 Brain-Stem 83.6324 10.1835 34.0000 108.0000 74.0000 12 17 3738 3442.8 Left-Hippocampus 74.7269 8.1358 40.0000 97.0000 57.0000 13 18 1100 1054.6 Left-Amygdala 76.2536 7.1347 43.0000 95.0000 52.0000 14 24 1791 1694.4 CSF 51.9894 11.2187 32.0000 94.0000 62.0000 15 26 278 249.5 Left-Accumbens-area 85.4928 6.2711 54.0000 93.0000 39.0000 16 28 4171 3992.6 Left-VentralDC 92.5809 11.1675 41.0000 116.0000 75.0000 17 30 0 0.0 Left-vessel 0.0000 0.0000 0.0000 0.0000 0.0000 18 31 928 888.8 Left-choroid-plexus 52.3438 10.8472 31.0000 78.0000 47.0000 19 43 20737 20900.1 Right-Lateral-Ventricle 37.1717 8.9953 25.0000 92.0000 67.0000 20 44 5481 5495.9 Right-Inf-Lat-Vent 37.8816 9.1653 26.0000 79.0000 53.0000 21 46 16633 17143.0 Right-Cerebellum-White-Matter 83.6901 5.3551 40.0000 99.0000 59.0000 22 47 54353 54454.1 Right-Cerebellum-Cortex 66.2976 9.1862 20.0000 89.0000 69.0000 23 49 6416 6042.8 Right-Thalamus-Proper 89.1852 9.9130 37.0000 106.0000 69.0000 24 50 3294 3062.4 Right-Caudate 87.1703 8.2085 53.0000 107.0000 54.0000 25 51 3794 3796.8 Right-Putamen 92.5113 4.1020 62.0000 104.0000 42.0000 26 52 2124 2028.5 Right-Pallidum 102.1172 4.1392 75.0000 118.0000 43.0000 27 53 2980 2742.1 Right-Hippocampus 73.9638 9.4803 28.0000 96.0000 68.0000 28 54 1299 1132.8 Right-Amygdala 69.1655 14.6045 28.0000 98.0000 70.0000 29 58 273 223.8 Right-Accumbens-area 88.0403 5.5989 64.0000 99.0000 35.0000 30 60 3924 3713.0 Right-VentralDC 92.1210 12.3974 35.0000 117.0000 82.0000 31 62 13 24.5 Right-vessel 60.4615 6.2930 48.0000 71.0000 23.0000 32 63 1302 1224.4 Right-choroid-plexus 51.1751 10.0901 31.0000 79.0000 48.0000 33 72 0 0.0 5th-Ventricle 0.0000 0.0000 0.0000 0.0000 0.0000 34 77 1508 1452.2 WM-hypointensities 74.0351 13.0445 37.0000 107.0000 70.0000 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000
Thank you!
Yongxiang Zhao Ph.D. student Radiology Department of Xuanwu Hospital, Capital Medical University
2014-2017 Xuanwu Hospital, Capital Medical University Postgraduate 2009-2014 Qingdao Medical College Undergraduate
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
赵永翔