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.
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.orsi@gmail.com
Thank you very much Bruce!
Have a nice day/night.
2011/10/3 Bruce Fischl fischl@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.orsi@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/**compliancelinehttp://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.
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 fischl@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.orsi@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/**compliancelinehttp://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.
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 fischl@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 BruceOn 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.orsi@gmail.comThe 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 . 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.orsi@gmail.com
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 fischl@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 fischl@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 BruceOn Mon, 3 Oct 2011, Gergely Orsi wrote:
Dear Freesurfers!! I've encountered two strange segmentation "errors", if they areerrors at all.
Please see the attached fs.png: You can see that there are excess pial tissues on the superior partof 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 redline).
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.orsi@gmail.comThe 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/**compliancelinehttp://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.orsi@gmail.com
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 fischl@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 <fischl@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.orsi@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 . 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.orsi@gmail.com-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
Yes of course, just a minute.
2011/10/25 Bruce Fischl fischl@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 fischl@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 <fischl@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.orsi@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.orsi@gmail.com-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
SZEMAN2.tar.gz have just been uploaded.
Thank you
Gergo
2011/10/25 Gergely Orsi gergo.orsi@gmail.com
Yes of course, just a minute.
2011/10/25 Bruce Fischl fischl@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 fischl@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 <fischl@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.orsi@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.orsi@gmail.com-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
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.orsi@gmail.com Yes of course, just a minute.
2011/10/25 Bruce Fischl fischl@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 <fischl@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 <fischl@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.orsi@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 . 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.orsi@gmail.com -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
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 fischl@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.orsi@gmail.com Yes of course, just a minute.
2011/10/25 Bruce Fischl fischl@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 22:38:51nicks 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 <fischl@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 <fischl@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.orsi@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.orsi@gmail.com -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
total brain volume would be a more conservative normalization - it would test the hypothesis that some brain regions are atrophying faster than average.
cheers Bruce On Thu, 27 Oct 2011, Gergely Orsi wrote:
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 fischl@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.orsi@gmail.com> Yes of course, just a minute. 2011/10/25 Bruce Fischl <fischl@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 <fischl@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 <fischl@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.orsi@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 . 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.orsi@gmail.com -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com-- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi@gmail.com
you can also check the accuracy of the registration used to compute the eTIV with:
cd $SUBJECTS_DIR/$subject/mri/transforms
tkregister2 --lta talairach_with_skull.lta \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk.reg.dat
doug
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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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.orsi@gmail.com <mailto:gergo.orsi@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 . 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.orsi@gmail.com mailto:gergo.orsi@gmail.com
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