Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature?
Thanks for your help! Laura
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
Hi Laura - Please read the information on the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 but in a newer update, that you can download from that wiki page.
As an aside, you should not be using recon-all from 5.2, since 5.3 was released immediately after to fix a bug in 5.2.
Hope this helps, a.y
On Fri, 13 Dec 2013, Laura Christine Anderson wrote:
Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature?
Thanks for your help! Laura
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
Hi Anastasia, thanks so much for your help. I downloaded the update to calculate motion parameters for each participant. I now have Freesurfer 5.3 installed on my server but all the preprocessing was completed in Freesurfer 5.1 (not 5.2 like I originally said). Can I run the motion calculation step (trac-all -qa) using preprocessed data from 5.1?
I tried and am getting this error message:
brain:/export/data/brain1/RSTOM: trac-all -qa -c /export/data/brain1/RSTOM/dmrirc.example_NEW_5.3 INFO: SUBJECTS_DIR is /export/data/brain1/RSTOM INFO: Diffusion root is /export/data/brain1/RSTOM Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/5.3.0/Linux-x64 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory /cell_root/software/freesurfer/new/sys/bin/dmri_group: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/new/sys Previous: /software/brain/Freesurfer/5.1.0/freesurfer/ trac-preproc -c /export/data/brain1/RSTOM/TLR103/scripts/dmrirc.local -log /export/data/brain1/RSTOM/TLR103/scripts/trac-all.log -cmd /export/data/brain1/RSTOM/TLR103/scripts/trac-all.cmd #------------------------------------- /cell_root/software/freesurfer/new/sys/bin/trac-preproc #------------------------------------- #@# Image quality assessment Mon Jan 13 15:19:04 EST 2014 /cell_root/software/freesurfer/new/sys/bin/dmri_motion --dwi /export/data/brain1/RSTOM/TLR103/dmri/dwi_orig.nii.gz --mat /export/data/brain1/RSTOM/TLR103/dmri/dwi.ecclog --bval /export/data/brain1/RSTOM/TLR103/dmri/bvals --out /export/data/brain1/RSTOM/TLR103/dmri/dwi_motion.txt /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Linux brain.umd.edu 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Jan 13 15:19:04 EST 2014
Thanks for your help!
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
On 12/17/13 4:33 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Laura - Please read the information on the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 but in a newer update, that you can download from that wiki page.
As an aside, you should not be using recon-all from 5.2, since 5.3 was released immediately after to fix a bug in 5.2.
Hope this helps, a.y
On Fri, 13 Dec 2013, Laura Christine Anderson wrote:
Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature?
Thanks for your help! Laura
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
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 Laura - In case you're still having this problem, it potentially means that you're using the centos6 build of 5.3 when you should be using the centos4 build instead. Can you please check which build of 5.1 you were using?
Thanks, a.y
On Mon, 13 Jan 2014, Laura Christine Anderson wrote:
Hi Anastasia, thanks so much for your help. I downloaded the update to calculate motion parameters for each participant. I now have Freesurfer 5.3 installed on my server but all the preprocessing was completed in Freesurfer 5.1 (not 5.2 like I originally said). Can I run the motion calculation step (trac-all -qa) using preprocessed data from 5.1?
I tried and am getting this error message:
brain:/export/data/brain1/RSTOM: trac-all -qa -c /export/data/brain1/RSTOM/dmrirc.example_NEW_5.3 INFO: SUBJECTS_DIR is /export/data/brain1/RSTOM INFO: Diffusion root is /export/data/brain1/RSTOM Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/5.3.0/Linux-x64 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory /cell_root/software/freesurfer/new/sys/bin/dmri_group: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/new/sys Previous: /software/brain/Freesurfer/5.1.0/freesurfer/ trac-preproc -c /export/data/brain1/RSTOM/TLR103/scripts/dmrirc.local -log /export/data/brain1/RSTOM/TLR103/scripts/trac-all.log -cmd /export/data/brain1/RSTOM/TLR103/scripts/trac-all.cmd #------------------------------------- /cell_root/software/freesurfer/new/sys/bin/trac-preproc #------------------------------------- #@# Image quality assessment Mon Jan 13 15:19:04 EST 2014 /cell_root/software/freesurfer/new/sys/bin/dmri_motion --dwi /export/data/brain1/RSTOM/TLR103/dmri/dwi_orig.nii.gz --mat /export/data/brain1/RSTOM/TLR103/dmri/dwi.ecclog --bval /export/data/brain1/RSTOM/TLR103/dmri/bvals --out /export/data/brain1/RSTOM/TLR103/dmri/dwi_motion.txt /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Linux brain.umd.edu 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Jan 13 15:19:04 EST 2014
Thanks for your help!
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
On 12/17/13 4:33 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Laura - Please read the information on the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 but in a newer update, that you can download from that wiki page.
As an aside, you should not be using recon-all from 5.2, since 5.3 was released immediately after to fix a bug in 5.2.
Hope this helps, a.y
On Fri, 13 Dec 2013, Laura Christine Anderson wrote:
Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature?
Thanks for your help! Laura
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
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 Anastasia, you are correct- that was the issue. All figured out now, thanks!
Laura
Sent from my iPhone
On Feb 5, 2014, at 6:57 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Laura - In case you're still having this problem, it potentially means that you're using the centos6 build of 5.3 when you should be using the centos4 build instead. Can you please check which build of 5.1 you were using?
Thanks, a.y
On Mon, 13 Jan 2014, Laura Christine Anderson wrote:
Hi Anastasia, thanks so much for your help. I downloaded the update to calculate motion parameters for each participant. I now have Freesurfer 5.3 installed on my server but all the preprocessing was completed in Freesurfer 5.1 (not 5.2 like I originally said). Can I run the motion calculation step (trac-all -qa) using preprocessed data from 5.1?
I tried and am getting this error message:
brain:/export/data/brain1/RSTOM: trac-all -qa -c /export/data/brain1/RSTOM/dmrirc.example_NEW_5.3 INFO: SUBJECTS_DIR is /export/data/brain1/RSTOM INFO: Diffusion root is /export/data/brain1/RSTOM Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/5.3.0/Linux-x64 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory /cell_root/software/freesurfer/new/sys/bin/dmri_group: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/new/sys Previous: /software/brain/Freesurfer/5.1.0/freesurfer/ trac-preproc -c /export/data/brain1/RSTOM/TLR103/scripts/dmrirc.local -log /export/data/brain1/RSTOM/TLR103/scripts/trac-all.log -cmd /export/data/brain1/RSTOM/TLR103/scripts/trac-all.cmd #------------------------------------- /cell_root/software/freesurfer/new/sys/bin/trac-preproc #------------------------------------- #@# Image quality assessment Mon Jan 13 15:19:04 EST 2014 /cell_root/software/freesurfer/new/sys/bin/dmri_motion --dwi /export/data/brain1/RSTOM/TLR103/dmri/dwi_orig.nii.gz --mat /export/data/brain1/RSTOM/TLR103/dmri/dwi.ecclog --bval /export/data/brain1/RSTOM/TLR103/dmri/bvals --out /export/data/brain1/RSTOM/TLR103/dmri/dwi_motion.txt /cell_root/software/freesurfer/new/sys/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Linux brain.umd.edu 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Jan 13 15:19:04 EST 2014
Thanks for your help!
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
On 12/17/13 4:33 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Laura - Please read the information on the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 but in a newer update, that you can download from that wiki page.
As an aside, you should not be using recon-all from 5.2, since 5.3 was released immediately after to fix a bug in 5.2.
Hope this helps, a.y
On Fri, 13 Dec 2013, Laura Christine Anderson wrote:
Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature?
Thanks for your help! Laura
Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Laura Christine Anderson