Sinead,
Much has improved since v4.5, so I would recommend updating to v5.2. I would have to re-run your prior subject data, as you will not be able to mix results processed with different versions, but any edits you made will be retained.
The mris_volmask failure you describe will not invalidate the results that it had produced for the subject up until the failure point (ie, the subcortical and cortical segmentations should be valid) but it does mean that stages downstream of that stage will not have run, and so some measures will not exist (likely even -segstats will not have run).
Nick
Hi Nick,
Thanks for your help. I'm running v4.5.0 on our cluster. I'm don't think the latest version has been installed. I might just ask them to install v5.2. Should I re-run the recon_all steps again with this latest version? Should I disregard the results that have already been computed with this error? I am still a Freesurfer beginner unfortunately so apologies for asking such questions!
Thanks again,
Sinead
On 4 March 2013 14:50, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Sinead
Are you running v5.0.0? This link has some info on fixing the problem, something your admin will have to do:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012846....
Or better yet you can them install install v5.2, which doesnt have that dependency in mris_volmask:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Nick
Dear members,
I am currently conducting cortical thickness analysis and I have ran
the
recon_all step. The appropriate files have been created including aseg.mgz, brainmask.mgz, aseg.stats etc. and therefore volumes and cortical thickness measures have been calculated, however, when I look at the output of
my
script it states that the job has exited with errors (see below)
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 001
mris_volmask.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Linux tcin-n05.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
EST
2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 1 20:00:42 GMT 2013
I'm not too sure what the error is or how to fix it. However, as the relevant files have been created, should I be too concerned about
this?
Also, I should mention that I am running my scripts on a high
performance
computing cluster and not locally on my linux.
Thank you for your help!
Sinead
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8