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 nicks@nmr.mgh.harvard.eduwrote:
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which will make just the files that are missing or out-of-date relative to their dependencies.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.
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