Hi Bruce and Nick, I think mri_gcut seems to require a lot of memory and might be causing the crash ? I was running some subjects on a node (16 cpu & 32 GB RAM ; thus 2GB RAM per cpu) and some of the subjects crashed for me at the mri_gcut step. (a few lines from recon-all.log are shown below) ---------------------------------------------------------------- mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz
terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.360000=39.600000 calculating weights... doing mincut... Abort --------------------------------------------------------------------- They worked if I assigned 4gb per cpu (Also i found i could run atmost 12 subjects with 32GB RAM).. maybe Michelle has a similar issue ? Mehul On Mon, Jan 24, 2011 at 1:56 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > is anything else running on the machine? Maybe some other process was > taking a bunch of memory while the gcut was running? > > On Mon, 24 Jan 2011, > Nick Schmansky wrote: > > > confirm that both T1.mgz and brainmask.auto.mgz a decent images (via > > tkmedit). if they are good, then the gcut stage can be skipped by > > adding the -no-gcut flag to the end of the recon-all stream, but i have > > never seen this particular error occur, so i wonder about the quality of > > the input. if those two files look fine, and gcut still gets killed > > (which is odd), then you can send me those files via our file drop and i > > can try to replicate. > > > > n. > > On Mon, 2011-01-24 at 15:01 -0500, Michelle Umali wrote: > >> Dear All, > >> recon-all was killed during mri_gcut. > >> > >> Here is the error: > >> > >> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz > >> > >> Killed. > >> > >> How does one deal with this? > >> > >> Thanks in advance for any help. > >> Michelle > >> _______________________________________________ > >> 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. > >
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