sure, that would be helpful 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 BruceI 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: HiAre 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.