Yes. This was our guess also, the problem is that these subject were scanned with an old MPRAGE sequence that has only 160 slices and 0.94mm slice thickness, thus it does not provide full brain coverage, part of the cerebellum is missing for the big headed subjects.
That is the main reason for the cerebellum cutoff. Is it a good idea to normalize the brain volumes (total gray m., total white m., ventricles, CSF) with brain mask volume instead of ICV? We just want to evaluate these 7 subjects, they have 2 time points (24 hours post injury and 3 months later) and want to compensate for different skull size. The volume values will be correlated with other parameters like MD, FA, LI, clinical scores, etc. They were all measured with the same non-Freesurfer optimized MPRAGE sequence (TR:1900ms, TE:3,41ms, FOV: 240mm, FOV Phase:87,5%, slice thickness: 0,94mm, number of slices :160, phase encoding direction: R->L, TI:900ms, flip angle:9° matrix:256×256, bandwith:180Hz/pixel, resolution: 0,94×0,94×0,94mm.) Can you suggest any other measured parameter that we can use to normalize the volumes? One more question, how can we assess the total left and right hemisphere' volume? Thank you very much. Gergo 2011/10/25 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > I think your acquisition is cutting off some cerebellum, and in any case > has a very steep intensity drop off in the cerebellum and brainstem. Is it > slab selective in that direction? You might try increasing the size of the > slab or lengthening your slab-select pulse, or including some oversampling > in that direction. > > > On Tue, 25 Oct 2011, Gergely Orsi wrote: > > 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 >> >> -- 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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