SZEMAN2.tar.gz have just been uploaded. Thank you
Gergo 2011/10/25 Gergely Orsi <gergo.o...@gmail.com> > 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 > -- 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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