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 wor
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)
--
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
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 tho
