Yes of course, just a minute. 2011/10/25 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> I meant canyou tar and gzip the subject and ftp it to us > > On Tue, 25 Oct 2011, Gergely Orsi wrote: > > 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 >> >> -- 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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