On 4 March 2013 16:55, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote:

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.html
>>
>> 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
>>
>>
>>
>> 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.
>>
>>
>>
>
>
> --
> Sinead Kelly
> Neuropsychiatric Genetics Group
> Trinity Centre
> St. James's Hospital
> Dublin 8
>

Sinead Kelly

Neuropsychiatric Genetics Group

Trinity Centre

St. James's Hospital

Dublin 8