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
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--
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
