Hi Knut
the best would be if you can just tar and gzip the entire subject dir and upload it according to these dirs:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers
Bruce
On Sat, 6 May 2017, Knut J Bjuland wrote:
Hi Bruce
Where should I upload orig.mgz, nu.mgz, aseg.mgz and voxel cords?
Knut Jørgen
____________________________________________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
Sent: Friday, May 5, 2017 4:44:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Differences in aseg volumes between FreeSurfer
5.3.0 and FreeSurfer 6.0
Include the orig.mgz and voxel cords and I'll see if I have already fixed it
On May 5, 2017, at 10:11 AM, Knut J Bjuland <knutjorgen@outlook.com> wrote:
Hi Bruce
I found some filled-in occipital horn and some in the anterior parts. I can
upload nu.mgz and aseg.mgz for a subject with problems with lateral ventri
cle.
Cheers
Knut Jørgen
On 4 May 2017, at 16:54, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
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
<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 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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