Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent left lateral ventricle from being filled with WM? Should I send the MPRAGE sequence information?
Knut Jørgen
On 2 May 2017, at 17:57, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@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 using this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSurfer 6.0. Are these differences larger than one would expect? I think that 100% may be a little high? The difference in volume between Freesurfer 5.3 and Freesurfer 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 <knutjorgen@outlook.commailto:knutjorgen@outlook.com> wrote:
Dear FreeSurfer expert,
I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 with asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I have enclosed the range for some of the volume. I found the largest differences in subcortical structures, especially in Corpus callosum(CC). I found that FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfer 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 the FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions of 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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