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
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
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
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 fischl@nmr.mgh.harvard.eduwrote:
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.
hmm, didnt think of that. i can experiment on some lesser memory machines. thanks for the info.
fyi, the gcut stage is not required, it only attempts additional 'trimming' of dura and surround skull that remains after mri_watershed, so adding -no-gcut to the end of recon-all is an acceptable workaround. i suppose recon-all could also not exit on mri_gcut failure due to out-of-memory (but this is a little hacky).
n.
On Mon, 2011-01-24 at 15:42 -0800, Mehul Sampat wrote:
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 fischl@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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Mehul Sampat -
Michelle Umali -
Nick Schmansky