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.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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