On Thu, Mar 18, 2010 at 1:22 PM, Sita Kakunoori <sita@nmr.mgh.harvard.edu> wrote:

Hi Mike,

Did you check the talairach. And how do nu.mgz and T1.mgz look.
Also you could probably try running the following command to see if the skull strip step finishes without errors.

recon-all -skullstrip -no-wsgcaatlas -s <subjid>

Sita.

On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Bruce, Nick,

I'm getting a segmentation fault that's crashing recon-all at the start of
the watershed during skull-stripping. I've tried this three times, once
starting the unpacking stream fresh from the raw dicoms, and it keeps
happening at exactly the same place. I've been reconstructing brains of
other subjects in the same directory all the while, so I don't think it's a
permissions issue of any sort.

Full recon-all log is atatched, but here's the section where it crashes:

*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=116 y=166 z=95 r=51
first estimation of the main basin volume: 585576 voxelsSegmentation
fault
Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010
x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010

And here's the OS data from the bugr script:

FREESURFER_HOME: /software/Freesurfer/4.4.0

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-20-generic x86_64

Do you have any idea what might be going wrong?

Thanks!
Mike

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