Hi Nick,
Thanks. i restarted as you recommended. My initial command had
a -lGI flag. Obviously, it will not be considered during this second run. I
do
not want to restart the process now, but i wanted to know if the GI can be
calculated
separately after all the stages of recon-all are done?
On a previous issue regarding the display (where only a part of the
rendering was visible)
we have managed (we think) to solve the problem, and get a proper display
over
the network, from a remote cluster. I will consolidate the steps that we
followed
and will send a mail around with this yet-another-solution.
thanks,
sid.
On Fri, Nov 21, 2008 at 3:45 PM, Nick Schmansky
<[EMAIL PROTECTED]>wrote:
> Sid,
>
> Firstly, make sure it didnt crash because of bad data. That is, if you
> can make the program that crashed crash again, check the input data. As
> for restarting, you can either use:
>
> recon-all -s subjid -make all
>
> which will make just the files that are missing or out-of-date relative
> to their dependencies. Or reference this chart:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
>
> and restart recon-all with just the flags used for the stages covering
> the parts that have not completed.
>
> In your case:
>
> recon-all -autorecon2-pial -autorecon3 -subjid subj
>
> would be appropriate, as that starts with the finalsurfs stage.
>
> Nick
>
>
> On Fri, 2008-11-21 at 15:37 -0800, Siddharth Srivastava wrote:
> > Hi again, everyone,
> > Apologies for another newbie question,
> > but i was wondering what is the best thing
> > to be done in case the program crashes in midflight, during the recon-
> > all invocation. As of now, i have
> > identified that the processing crashed sometime during
> > mris_make_surfaces (stage 21?). Is there any way
> > i can restart the process from this point? or, what is the most
> > optimal strategy?
> > regards,
> > sid.
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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