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)

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline%C2%A0. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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)

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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 ventricle.

Cheers Knut Jørgen

On 4 May 2017, at 16:54, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto: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.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 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.commailto: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) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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.commailto: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 ventricle.

Cheers Knut Jørgen

On 4 May 2017, at 16:54, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto: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.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 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.commailto: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) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Bruce

I have uploaded the subject as subject_7.tar.gz and subject_7.zip at transfer/incoming on surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ I can also upload the same subject where I used fs53.

Thanks Knut Jørgen

On 7 May 2017, at 16:26, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

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) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

p.s. did 5.3 do better? Did you try it with -bigventricles? The ventricles on this subject are extremely large. On Sun, 7 May 2017, Knut J Bjuland wrote:

Hi Bruce

I have uploaded the subject as subject_7.tar.gz and subject_7.zip at transf er/incoming on surfer.nmr.mgh.harvard.edu I can also upload the same subject where I used fs53.

Thanks Knut Jørgen

  On 7 May 2017, at 16:26, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu> wrote:

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 ra n

?? ?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)
       _______________________________________________
       Freesurfer mailing list
       Freesurfer@nmr.mgh.harvard.edu
       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
       The information in this e-mail is intended only for
       the
       person to whom it is
       addressed. If you believe this e-mail was sent to
       you in
       error and the e-mail
       contains patient information, please contact the
       Partners
       Compliance HelpLine at
       http://www.partners.org/complianceline . If the
       e-mail was
       sent to you in error
       but does not contain patient information, please
       contact
       the sender and properly
       dispose of the e-mail.
       _______________________________________________
       Freesurfer mailing list
       Freesurfer@nmr.mgh.harvard.edu
       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
       _______________________________________________
       Freesurfer mailing list
       Freesurfer@nmr.mgh.harvard.edu
       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
       The information in this e-mail is intended only for
       the person to whom
       it is
       addressed. If you believe this e-mail was sent to
       you in error and the
       e-mail
       contains patient information, please contact the
       Partners Compliance
       HelpLine at
       http://www.partners.org/complianceline . If the
       e-mail was sent to you
       in error
       but does not contain patient information, please
       contact the sender
       and properly
       dispose of the e-mail.
  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  The information in this e-mail is intended only for the
  person
  to whom it is
  addressed. If you believe this e-mail was sent to you in
  error
  and the e-mail
  contains patient information, please contact the Partners
  Compliance HelpLine at
  http://www.partners.org/complianceline . If the e-mail was
  sent
  to you in error
  but does not contain patient information, please contact
  the
  sender and properly
  dispose of the e-mail.

       _______________________________________________
       Freesurfer mailing list
       Freesurfer@nmr.mgh.harvard.edu
       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi,  In my dataset, the lateral ventricles are filled in the wm.mgz (picture). However the aseg.mgz shows that these voxels were correctly classified as lateral ventricles. In another thread on this mailing list, I was advised to fill in the ventricular voxels as wm.mgz if the surfaces are not correct. Am I doing something wrongly?

Thanks.

On Thursday, May 4, 2017 10:18 AM, Knut J Bjuland knutjorgen@outlook.com wrote:

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.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.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) |

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline%C2%A0. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.