Hi Knut
I didn't see a 100% below. They look like what we usually see - low contrast small structures (e.g. the pallidum) or ones with poorly definied boundaries (the segments of the callosum, also quite small) show large % changes (which typically correspond to not very many voxels).
cheers Bruce
On Tue, 2 May 2017, 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 <knutjorgen@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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