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
>>
>>
>
>
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