Here you are: # 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 SZEMAN2 --surf-wm-vol --ctab /home/kutato/freesurfer/ASegStatsLUT.txt # sysname Linux # hostname kutato16 # machine x86_64 # user kutato16 # anatomy_type volume # # SUBJECTS_DIR /home/kutato/freesurfer/subjects # subjectname SZEMAN2 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2011/09/30 14:48:41 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 964476.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 986721, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 986721.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2011/09/30 21:17:55 # ColorTable /home/kutato/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2009/08/11 14:24:37 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2011/09/30 15:23:28 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2011/09/30 15:23:28 # surface-based-volume mm3 lh-cerebral-white-matter 199672.312500 # surface-based-volume mm3 rh-cerebral-white-matter 200666.875000 # surface-based-volume mm3 tot-cerebral-white-matter 400339.187500 # 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 181224 181224.0 Left-Cerebral-White-Matter 103.0824 7.8273 37.0000 124.0000 87.0000 2 3 220289 220289.0 Left-Cerebral-Cortex 73.9965 10.0547 25.0000 109.0000 84.0000 3 4 9827 9827.0 Left-Lateral-Ventricle 38.7152 10.8311 21.0000 89.0000 68.0000 4 5 472 472.0 Left-Inf-Lat-Vent 58.1272 10.0729 36.0000 97.0000 61.0000 5 7 11866 11866.0 Left-Cerebellum-White-Matter 85.2734 7.6396 41.0000 110.0000 69.0000 6 8 29669 29669.0 Left-Cerebellum-Cortex 62.3768 10.6794 17.0000 94.0000 77.0000 7 10 6422 6422.0 Left-Thalamus-Proper 97.5967 8.1825 54.0000 114.0000 60.0000 8 11 3645 3645.0 Left-Caudate 86.3108 8.2356 52.0000 110.0000 58.0000 9 12 5670 5670.0 Left-Putamen 93.1821 5.7430 62.0000 111.0000 49.0000 10 13 1860 1860.0 Left-Pallidum 105.5083 3.8920 85.0000 116.0000 31.0000 11 14 1023 1023.0 3rd-Ventricle 46.9565 12.7555 28.0000 78.0000 50.0000 12 15 1027 1027.0 4th-Ventricle 34.1996 12.3672 11.0000 73.0000 62.0000 13 16 12081 12081.0 Brain-Stem 91.9390 11.8567 44.0000 113.0000 69.0000 14 17 2538 2538.0 Left-Hippocampus 80.2219 8.1671 29.0000 109.0000 80.0000 15 18 952 952.0 Left-Amygdala 80.3787 7.1404 55.0000 105.0000 50.0000 16 24 1785 1785.0 CSF 57.1199 13.1850 29.0000 95.0000 66.0000 17 26 592 592.0 Left-Accumbens-area 84.8315 5.7364 60.0000 104.0000 44.0000 18 28 3806 3806.0 Left-VentralDC 101.0622 9.6848 51.0000 115.0000 64.0000 19 30 190 190.0 Left-vessel 71.0192 10.0774 43.0000 96.0000 53.0000 20 31 1895 1895.0 Left-choroid-plexus 54.4754 12.4270 24.0000 96.0000 72.0000 21 41 188053 188053.0 Right-Cerebral-White-Matter 101.6959 7.7683 38.0000 122.0000 84.0000 22 42 216751 216751.0 Right-Cerebral-Cortex 73.3417 9.8270 24.0000 106.0000 82.0000 23 43 9286 9286.0 Right-Lateral-Ventricle 39.9627 11.6894 21.0000 93.0000 72.0000 24 44 246 246.0 Right-Inf-Lat-Vent 50.3990 10.5551 27.0000 78.0000 51.0000 25 46 11000 11000.0 Right-Cerebellum-White-Matter 87.6621 6.5420 44.0000 108.0000 64.0000 26 47 36257 36257.0 Right-Cerebellum-Cortex 65.1387 10.4182 21.0000 94.0000 73.0000 27 49 6546 6546.0 Right-Thalamus-Proper 97.0832 8.3261 54.0000 114.0000 60.0000 28 50 3700 3700.0 Right-Caudate 84.7295 8.0259 48.0000 116.0000 68.0000 29 51 4879 4879.0 Right-Putamen 92.2331 5.6211 64.0000 111.0000 47.0000 30 52 1459 1459.0 Right-Pallidum 104.8717 3.4972 88.0000 114.0000 26.0000 31 53 3925 3925.0 Right-Hippocampus 78.0625 7.5244 49.0000 107.0000 58.0000 32 54 1406 1406.0 Right-Amygdala 79.3659 6.0069 55.0000 107.0000 52.0000 33 58 604 604.0 Right-Accumbens-area 88.0638 5.7372 60.0000 108.0000 48.0000 34 60 3824 3824.0 Right-VentralDC 100.9456 10.2128 47.0000 113.0000 66.0000 35 62 72 72.0 Right-vessel 69.6552 6.7526 55.0000 84.0000 29.0000 36 63 1781 1781.0 Right-choroid-plexus 56.6733 10.7892 27.0000 93.0000 66.0000 37 72 12 12.0 5th-Ventricle 63.1875 6.7352 52.0000 75.0000 23.0000 38 77 1148 1148.0 WM-hypointensities 78.2284 11.3100 44.0000 109.0000 65.0000 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 28 28.0 non-WM-hypointensities 65.2750 11.5603 45.0000 89.0000 44.0000 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 85 344 344.0 Optic-Chiasm 85.2781 19.9109 32.0000 116.0000 84.0000 45 251 700 700.0 CC_Posterior 111.7594 8.1882 77.0000 119.0000 42.0000 46 252 319 319.0 CC_Mid_Posterior 104.1261 12.7185 65.0000 119.0000 54.0000 47 253 325 325.0 CC_Central 107.0531 9.7545 73.0000 119.0000 46.0000 48 254 348 348.0 CC_Mid_Anterior 106.5294 9.0198 80.0000 119.0000 39.0000 49 255 752 752.0 CC_Anterior 107.1329 9.3344 65.0000 120.0000 55.0000
2011/10/25 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > can you send us an example of one that is way off? > > On Tue, 25 Oct 2011, Gergely Orsi wrote: > > Dear Bruce and others, >> >> We have just ran into strange ICV volumes. >> >> For all our 100+ subjets, the total icv is around 1500cm3 (around >> 1300-1700). >> >> For the new group (only 7 subjects) the average ICV is around 1200 >> (ranging from 900-1500). >> >> This is almost microcephalia, but they are normal. >> >> If we take a look at the brainseg volume or brain mask volumes they are >> larger than the total ICV (for e.g. subject 5 has brainmaskvol: 1440; >> brainseg >> vol: 1021; ICV 1036) >> >> This is not right. It's kind'a strange that someone has bigger brain than >> skull :) >> >> I was using freesurfer 4.5 for both groups. >> >> >> Do you have any idea what did I miss? >> >> Thanks, >> >> Gergo >> >> >> >> >> >> >> >> 2011/10/3 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> The stuff outside the pial surface won't affect things, which is one >> of the reasons we prefer the surface-based measured of cortical >> morphometry. >> >> Similarly, we don't use the surface-based stuff in the hippocampus, >> so you should be all set (since many of the cortical assumptions aren't >> valid there) >> >> cheers >> Bruce >> >> >> >> On Mon, 3 Oct 2011, Gergely Orsi wrote: >> >> Dear Freesurfers!! >> >> I've encountered two strange segmentation "errors", if they are >> errors at >> all. >> >> >> >> Please see the attached fs.png: >> >> You can see that there are excess pial tissues on the superior part >> of the >> brain. The pial surface is >> defined correctly and the excess pial tissue is outside the red line >> yet it >> is coloured pink. My question, is : >> >> Does this have any impact on the results? >> >> >> The second is related to the hippocampus. >> >> Please see the attached fs2.png: >> >> The pial surface around the hippocampus looks a bit weird. >> It actually discards 1/3 of the hippocampus (it is outside the red >> line). >> >> Do you have any suggestions regarding the two problems. >> >> I'm using FS 4.5 on several 64bit linux distributions. >> >> >> -- >> Gergely Orsi >> biologist - research associate >> Diagnostic Center of Pécs >> H-7623 Pécs, Rét str. 2. >> Tel.: 0036-70-3174676 >> E-mail: gergo.o...@gmail.com >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> >> -- >> Gergely Orsi >> biologist - research associate >> Diagnostic Center of Pécs >> H-7623 Pécs, Rét str. 2. >> Tel.: 0036-70-3174676 >> E-mail: gergo.o...@gmail.com >> >> -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.o...@gmail.com
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