Mia, this time it looks like there was plenty of memory, but it exited on a defect. make sure the wm.mgz looks good (doesnt have stuff outside the white matter). see the 'topological defects' section of our tutorial for info on what to look for and how to fix it.
Nick > Hi freesurfers, > > So i reran recon-all -make all overnight, and it ended with errors still. > It looks like the same error (I attached the log). There was another > process running while I ran the recon the first time, but I made sure that > wasn't the case this time around. Is the solution running the recon in a > whole new place with more space? > > Thanks so much, > m > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky > [ni...@nmr.mgh.harvard.edu] > Sent: Wednesday, January 23, 2013 1:45 PM > To: Douglas N Greve > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Memory problem > > Mia, > > also i noticed this at the top of the log: > > total used free > Mem: 37010736 19490372 17520364 > -/+ buffers/cache: 10784236 26226500 > Swap: 8393952 150528 8243424 > > > it shows that just 1.7GB is available for the recon to run, which is > below what we recommend. recon-all usually needs at least 2GB. > > after inspecting for defects like doug suggests, you could try stopping > other apps that are consuming mem (or just reboot which will ensure > maximal free memory) and then run recon-all -make all > > Nick > > > > > On Wed, 2013-01-23 at 13:23 -0500, Douglas N Greve wrote: >> Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge >> defect (like the entire cerebellum is attached). You can run >> >> tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix >> >> Note that you will get a few error messages when loading the orig.nofix >> surface. These can be ignored >> >> doug >> >> On 01/23/2013 12:19 PM, Borzello, Mia wrote: >> > Hey Freesurfers, >> > >> > I received a "Cannot allocate memory" error while running a recon >> overnight. I think there should be enough space on the machine to >> store the data so I'm suspicious that it's a different memory problem. >> > I attached the recon-all.log file. >> > >> > Thanks for your help! >> > m >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
