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