we use smriprep for structural preprocessing and surface reconstruction on our local HPC. It contains freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a.
The image outputs look flawless. However, BrainSeg and BrainSegNotVent reported in aseg.stats are far above expected values (for instance larger than eTIV; example output attached).
We have processed 600 subjects and the issue applies to all of them. We are currently trying to reproduce these results with freesurfer on a local machine to make sure it's not flawed data or smriprep that is responsible for the issue.
As computing brain volume by hand with aseg.mgz yields sensible results (~1.3 mio mm³) we consider mri_segstats in smriprep to be the problem.
Grateful for any input.
# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --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 --euler --ctab /work/fatx405/local/freesurfer-6.0.0/ASegStatsLUT.txt --subject sub-003db57e
# sysname Linux
# hostname node001
# machine x86_64
# user fatx405
# anatomy_type volume
#
# SUBJECTS_DIR /work/fatx405/projects
# subjectname sub-003db57e
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 2142619.000000, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 2096581.000000, mm^3
# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1306062.635541, mm^3
# Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 39720.000000, mm^3
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 243502.815347, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 247635.016739, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 491137.832086, mm^3
# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 229977.705303, mm^3
# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 231861.098152, mm^3
# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 461838.803455, mm^3
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 97441.000000, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 789956.832086, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1083680.635541, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1043960.635541, mm^3
# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 1840953.000000, mm^3
# Measure Mask, MaskVol, Mask Volume, 2714626.000000, mm^3
# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 1.272865, unitless
# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 1.612677, unitless
# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 37, unitless
# Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 25, unitless
# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 62, unitless
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1683304.717707, mm^3
# SegVolFile mri/aseg.mgz
# SegVolFileTimeStamp 2021/08/19 16:13:35
# ColorTable /work/fatx405/local/freesurfer-6.0.0/ASegStatsLUT.txt
# ColorTableTimeStamp 2018/08/13 14:53:06
# InVolFile mri/norm.mgz
# InVolFileTimeStamp 2021/08/19 16:13:32
# InVolFrame 0
# PVVolFile mri/norm.mgz
# PVVolFileTimeStamp 2021/08/19 16:13:32
# Excluding Cortical Gray and White Matter
# ExcludeSegId 0 2 3 41 42
# VoxelVolume_mm3 0.578704
# 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 20298 11994.6 Left-Lateral-Ventricle 27.8315 11.9737 11.0000 93.0000 82.0000
2 5 500 344.7 Left-Inf-Lat-Vent 45.6800 12.3120 15.0000 78.0000 63.0000
3 7 27409 16402.5 Left-Cerebellum-White-Matter 82.5499 5.4997 37.0000 97.0000 60.0000
4 8 96661 55934.2 Left-Cerebellum-Cortex 62.4935 9.7135 0.0000 133.0000 133.0000
5 10 13493 7617.2 Left-Thalamus-Proper 90.8387 9.8593 30.0000 114.0000 84.0000
6 11 5022 2935.7 Left-Caudate 83.4389 8.1582 38.0000 107.0000 69.0000
7 12 7212 4143.9 Left-Putamen 91.5836 7.3237 47.0000 109.0000 62.0000
8 13 3570 2071.3 Left-Pallidum 103.8275 4.9761 56.0000 119.0000 63.0000
9 14 2192 1353.2 3rd-Ventricle 32.0027 11.5672 15.0000 79.0000 64.0000
10 15 1986 1251.9 4th-Ventricle 35.6591 12.4108 12.0000 76.0000 64.0000
11 16 41250 24051.8 Brain-Stem 81.4896 9.2479 22.0000 111.0000 89.0000
12 17 7369 4120.0 Left-Hippocampus 72.6194 8.3441 33.0000 106.0000 73.0000
13 18 3042 1695.2 Left-Amygdala 71.5999 6.1066 37.0000 99.0000 62.0000
14 24 2140 1185.9 CSF 43.4280 13.4853 16.0000 89.0000 73.0000
15 26 666 384.1 Left-Accumbens-area 78.7327 4.1748 55.0000 92.0000 37.0000
16 28 7719 4298.9 Left-VentralDC 91.9097 10.6368 29.0000 121.0000 92.0000
17 30 181 126.6 Left-vessel 54.9834 12.0437 28.0000 77.0000 49.0000
18 31 1531 819.7 Left-choroid-plexus 49.5532 11.3961 22.0000 81.0000 59.0000
19 43 15549 9136.9 Right-Lateral-Ventricle 29.6998 13.2484 9.0000 94.0000 85.0000
20 44 403 267.4 Right-Inf-Lat-Vent 45.0025 12.8842 16.0000 80.0000 64.0000
21 46 26601 15867.2 Right-Cerebellum-White-Matter 82.2607 5.5614 35.0000 97.0000 62.0000
22 47 99608 57495.8 Right-Cerebellum-Cortex 62.0247 9.5405 17.0000 106.0000 89.0000
23 49 13412 7495.8 Right-Thalamus-Proper 87.9864 9.8004 31.0000 110.0000 79.0000
24 50 5187 3006.0 Right-Caudate 81.9400 8.5023 44.0000 105.0000 61.0000
25 51 7601 4339.7 Right-Putamen 89.1673 7.5487 44.0000 109.0000 65.0000
26 52 3692 2139.9 Right-Pallidum 102.9976 4.7986 61.0000 117.0000 56.0000
27 53 7445 4205.5 Right-Hippocampus 71.2660 7.9302 27.0000 99.0000 72.0000
28 54 3503 1970.0 Right-Amygdala 71.8310 5.9510 43.0000 100.0000 57.0000
29 58 849 475.8 Right-Accumbens-area 79.5324 5.1089 62.0000 99.0000 37.0000
30 60 7709 4301.8 Right-VentralDC 91.0214 11.1633 24.0000 117.0000 93.0000
31 62 76 55.6 Right-vessel 55.0132 13.2991 26.0000 75.0000 49.0000
32 63 1439 795.1 Right-choroid-plexus 48.4830 10.2814 17.0000 78.0000 61.0000
33 72 0 0.0 5th-Ventricle 0.0000 0.0000 0.0000 0.0000 0.0000
34 77 2497 1370.8 WM-hypointensities 73.4529 12.6269 14.0000 113.0000 99.0000
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 0 0.0 non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000
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 85 248 153.8 Optic-Chiasm 78.9476 17.7778 26.0000 115.0000 89.0000
41 251 1428 779.4 CC_Posterior 101.7458 17.1102 32.0000 121.0000 89.0000
42 252 734 379.2 CC_Mid_Posterior 93.2657 16.0395 36.0000 114.0000 78.0000
43 253 759 388.9 CC_Central 93.6245 16.6766 41.0000 113.0000 72.0000
44 254 785 422.7 CC_Mid_Anterior 100.7949 14.9042 47.0000 116.0000 69.0000
45 255 1539 836.8 CC_Anterior 100.6595 16.0710 32.0000 121.0000 89.0000