Hi Antonin, I think this is a bug. Can you send me the recon-all.log file? thanks doug
On 4/1/19 5:49 PM, Antonin Skoch wrote: > > External Email - Use Caution > > Dear experts, > > I noticed suspicious values of segmentation volume in aseg.stats in > subjects processed with version 6, with recon-all modified for HCP data. > > There is striking difference between BrainSegVolNotVent and > BrainSegVolNotVentSurf. The values of BrainSegVolNotVent seem > implasibly high. See example values of one of my subjects: > > > # 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 /my_freesurfer_home/ASegStatsLUT.txt > --subject mysubj > # sysname Linux > # hostname myhost > # machine x86_64 > # user skoch > # anatomy_type volume > # > # SUBJECTS_DIR /my_subjects > # subjectname mysubj > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, > 3474569.000000, mm^3 > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation > Volume Without Ventricles, 3432059.000000, mm^3 > # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain > Segmentation Volume Without Ventricles from Surf, 1444546.289023, mm^3 > # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of > ventricles and choroid plexus, 33665.000000, mm^3 > # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter > volume, 268625.129703, mm^3 > # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter > volume, 268347.204256, mm^3 > # Measure Cortex, CortexVol, Total cortical gray matter volume, > 536972.333959, mm^3 > # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left > hemisphere cerebral white matter volume, 158213.556983, mm^3 > # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right > hemisphere cerebral white matter volume, 156867.398082, mm^3 > # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral > white matter volume, 315080.955064, mm^3 > # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, > 159729.000000, mm^3 > # Measure TotalGray, TotalGrayVol, Total gray matter volume, > 1034461.333959, mm^3 > # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, > 1036297.289023, mm^3 > # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, > Supratentorial volume, 1002632.289023, mm^3 > # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, > Supratentorial volume voxel count, 2998814.000000, mm^3 > # Measure Mask, MaskVol, Mask Volume, 5060060.000000, mm^3 > # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of > BrainSegVol to eTIV, 2.172140, unitless > # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, > 3.163315, unitless > # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh > surfaces prior to fixing, 62, unitless > # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh > surfaces prior to fixing, 48, unitless > # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in > surfaces prior to fixing, 110, unitless > # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total > Intracranial Volume, 1599606.583237, mm^3 > # SegVolFile mri/aseg.mgz > # SegVolFileTimeStamp 2018/05/09 15:43:12 > # ColorTable /my_freesurfer_home/ASegStatsLUT.txt > # ColorTableTimeStamp 2017/01/18 23:00:02 > # InVolFile mri/norm.mgz > # InVolFileTimeStamp 2018/05/07 13:29:02 > # InVolFrame 0 > # PVVolFile mri/norm.mgz > # PVVolFileTimeStamp 2018/05/07 13:29:02 > # Excluding Cortical Gray and White Matter > # ExcludeSegId 0 2 3 41 42 > # VoxelVolume_mm3 0.343 > # 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 14344 5109.0 Left-Lateral-Ventricle 33.1230 > 13.9291 5.0000 93.0000 88.0000 > 2 5 1383 503.7 Left-Inf-Lat-Vent 40.0911 14.4387 > 10.0000 86.0000 76.0000 > 3 7 38137 13247.3 Left-Cerebellum-White-Matter 80.9953 > 6.2349 21.0000 97.0000 76.0000 > 4 8 165378 56702.4 Left-Cerebellum-Cortex 63.3988 > 8.4866 13.0000 93.0000 80.0000 > 5 10 21580 7298.1 Left-Thalamus-Proper 86.6751 > 10.0317 34.0000 112.0000 78.0000 > 6 11 11020 3773.5 Left-Caudate 75.3689 7.7926 > 39.0000 107.0000 68.0000 > 7 12 12372 4236.2 Left-Putamen 81.2602 6.8960 > 41.0000 108.0000 67.0000 > 8 13 5644 1867.1 Left-Pallidum 90.9569 6.9118 > 39.0000 109.0000 70.0000 > 9 14 1863 663.4 3rd-Ventricle 38.3065 13.2033 > 11.0000 73.0000 62.0000 > 10 15 4110 1458.1 4th-Ventricle 31.4457 11.5906 > 11.0000 73.0000 62.0000 > 11 16 57498 19626.8 Brain-Stem 80.1195 8.8419 > 17.0000 111.0000 94.0000 > 12 17 11009 3687.8 Left-Hippocampus 64.4524 7.7197 > 21.0000 96.0000 75.0000 > 13 18 3836 1299.8 Left-Amygdala 62.8180 6.4462 > 33.0000 83.0000 50.0000 > 14 24 2872 958.5 CSF 44.5933 13.6240 15.0000 > 97.0000 82.0000 > 15 26 1621 547.5 Left-Accumbens-area 70.0956 > 6.6855 21.0000 87.0000 66.0000 > 16 28 12429 4141.1 Left-VentralDC 85.4310 10.3448 > 19.0000 108.0000 89.0000 > 17 30 49 25.9 Left-vessel 56.8163 7.2935 > 32.0000 69.0000 37.0000 > 18 31 1120 372.4 Left-choroid-plexus 53.3348 > 11.7100 18.0000 86.0000 68.0000 > 19 43 14869 5206.5 Right-Lateral-Ventricle 33.5337 > 14.0357 7.0000 91.0000 84.0000 > 20 44 657 266.5 Right-Inf-Lat-Vent 45.2953 12.1767 > 17.0000 88.0000 71.0000 > 21 46 56785 19552.6 Right-Cerebellum-White-Matter > 77.5366 9.1843 19.0000 100.0000 81.0000 > 22 47 163433 56188.2 Right-Cerebellum-Cortex 63.3668 > 8.8083 16.0000 95.0000 79.0000 > 23 49 20893 6985.6 Right-Thalamus-Proper 86.0407 > 10.3032 27.0000 111.0000 84.0000 > 24 50 11145 3814.2 Right-Caudate 74.8492 7.5833 > 45.0000 103.0000 58.0000 > 25 51 14128 4888.6 Right-Putamen 80.7402 6.5321 > 44.0000 104.0000 60.0000 > 26 52 5341 1736.3 Right-Pallidum 93.4239 6.1032 > 46.0000 109.0000 63.0000 > 27 53 11399 3861.1 Right-Hippocampus 65.9275 7.3061 > 34.0000 102.0000 68.0000 > 28 54 4239 1412.2 Right-Amygdala 63.2640 6.9283 > 30.0000 102.0000 72.0000 > 29 58 1510 510.4 Right-Accumbens-area 71.0742 > 5.3612 48.0000 93.0000 45.0000 > 30 60 11723 3884.1 Right-VentralDC 86.7650 10.9309 > 23.0000 111.0000 88.0000 > 31 62 33 17.0 Right-vessel 56.2727 8.0478 > 39.0000 73.0000 34.0000 > 32 63 1310 439.3 Right-choroid-plexus 53.4656 > 12.4803 23.0000 85.0000 62.0000 > 33 72 0 0.0 5th-Ventricle 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 34 77 2290 713.0 WM-hypointensities 71.8258 11.6413 > 36.0000 105.0000 69.0000 > 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 85 576 208.2 Optic-Chiasm 73.1979 15.5846 > 28.0000 100.0000 72.0000 > 41 251 2189 711.4 CC_Posterior 103.1558 13.1432 > 40.0000 120.0000 80.0000 > 42 252 1288 409.4 CC_Mid_Posterior 97.6079 16.6021 > 26.0000 120.0000 94.0000 > 43 253 1703 556.6 CC_Central 89.3676 13.4535 > 38.0000 111.0000 73.0000 > 44 254 1529 492.8 CC_Mid_Anterior 94.3931 14.5866 > 28.0000 119.0000 91.0000 > 45 255 2421 802.6 CC_Anterior 98.2759 13.0648 > 29.0000 118.0000 89.0000 > > It is in all my processed subjects. Could you please comment on? > > Thank you in advance, > > Antonin Skoch > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
