Hi Knut
where is it being filled? If it is the occipital horn we may soon have a
patch for it
cheers
Bruce
On Thu, 4 May 2017, Knut J Bjuland wrote:
Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent lef
t lateral ventricle from being filled with WM? Should I send the MPRAGE seq
uence information?
Knut Jørgen
On 2 May 2017, at 17:57, Douglas Greve
<gr...@nmr.mgh.harvard.edu> wrote:
This is a test we do before we release. The averages don't look out of
line. Putamen should be smaller because we now try to remove
claustrum. Small structures may have some large percent differences.
Some structures are not that meaningful (like the CC because it has no
real boundaries). The left lateral ventricle may be a problem. I've
seen cases where it totally gets filled in with WM in v6. Others are
hard to define -- when I would look at the scans there would not be a
good case for rejecting one and accepting the other (eg, pallidum and
thalamus don't have good contrast at typical mprage acq parameters).
On 5/2/17 3:56 AM, Knut J Bjuland wrote:
Dear FreeSurfer experts,
When I ran Freesurfer 5.3 and Freesurfer 6.0 I ran with default settings us
ing this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSu
rfer 6.0.
Are these differences larger than one would expect? I think that 100% may b
e a little high? The difference in volume between Freesurfer 5.3 and Freesu
rfer 6.0 is shown in the table below calculated using asegstatsdiff.
Knut Jørgen Bjuland
Volume name
Mean(range)
Left-Lateral-Ventricle
7.4 (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64 (-22.9,56.15)
Left-Cerebellum-Cortex
7.56 (-10.3,19.17)
Left-Thalamus-Proper
0.12 (-16.31,32.42)
Left-Caudate
-4.25 (-12,33.64)
Left-Putamen
-16.72 (-27.99,8.3)
Left-Pallidum
16.23 (-22.94,84.75)
Left-Hippocampus
-1.74 (-13.53,15.93)
Left-Amygdala
2.29 (-19.28,41.04)
Right-Lateral-Ventricle
4.6 (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2 (-20.87,49.37)
Right-Cerebellum-Cortex
4.88 (-12.99,14.36)
Right-Thalamus-Proper
1.06 (-22.34,19.99)
Right-Caudate
-6.08 (-14.59,6.13)
Right-Putamen
-12.87 (-31.37,10.17)
Right-Pallidum
14.01 (-27.79,89.19)
Right-Hippocampus
-1.71 (-9.29,12.02)
Right-Amygdala
3.74 (-18.6,51.01)
Right-Accumbens-area
-9.14 (-37.89,61.02)
CC_Posterior
22.07 (-47.04,525.51)
CC_Mid_Posterior
53.59 (-11.3,537.3)
CC_Central
36.77 (-21.36,317.24)
CC_Mid_Anterior
24.09 (-18.86,128.31)
CC_Anterior
10.64 (-33.71,152.33)
lhCortexVol
3.13 (-1.31,12.37)
rhCortexVol
3.16 (-0.36,14.2)
CortexVol
3 (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65 (-0.05,26.52)
On 21 Apr 2017, at 20:01, Knut J Bjuland
<knutjor...@outlook.com> wrote:
Dear FreeSurfer expert,
I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 w
ith asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I ha
ve enclosed the range for some of the volume. I found the largest differenc
es in subcortical structures, especially in Corpus callosum(CC). I found th
at FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfe
r 5.3. Nevertheless, these differences were much smaller for lhCortex, but
?? ?also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran t
he FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions o
f FreeSurfer were run on Centos. I am also enclosing a
table with mean values along with min and max for
differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg
volumes.
Best regards
Knut Jørgen Bjuland PhD
NTNU
Left-Lateral-Ventricle
7.4 (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64 (-22.9,56.15)
Left-Cerebellum-Cortex
7.56 (-10.3,19.17)
Left-Thalamus-Proper
0.12 (-16.31,32.42)
Left-Caudate
-4.25 (-12,33.64)
Left-Putamen
-16.72 (-27.99,8.3)
Left-Pallidum
16.23 (-22.94,84.75)
Left-Hippocampus
-1.74 (-13.53,15.93)
Left-Amygdala
2.29 (-19.28,41.04)
Right-Lateral-Ventricle
4.6 (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2 (-20.87,49.37)
Right-Cerebellum-Cortex
4.88 (-12.99,14.36)
Right-Thalamus-Proper
1.06 (-22.34,19.99)
Right-Caudate
-6.08 (-14.59,6.13)
Right-Putamen
-12.87 (-31.37,10.17)
Right-Pallidum
14.01 (-27.79,89.19)
Right-Hippocampus
-1.71 (-9.29,12.02)
Right-Amygdala
3.74 (-18.6,51.01)
Right-Accumbens-area
-9.14 (-37.89,61.02)
CC_Posterior
22.07 (-47.04,525.51)
CC_Mid_Posterior
53.59 (-11.3,537.3)
CC_Central
36.77 (-21.36,317.24)
CC_Mid_Anterior
24.09 (-18.86,128.31)
CC_Anterior
10.64 (-33.71,152.33)
lhCortexVol
3.13 (-1.31,12.37)
rhCortexVol
3.16 (-0.36,14.2)
CortexVol
3 (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65 (-0.05,26.52)
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