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
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