Hi Sita, all,

I got the rest of the recon to run, made pial edits on the brainmask after autorecon2, and then reran it to the end.  It looks like the reconstruction of the cortical surfaces and the inflation worked fine, but the cortical parcellation is totally scrambled.  I'm attatching an image of the inflated left hemisphere with the aparc annotation overlay.  (It looks much the same on the right hemisphere).  I'm also attaching the recon-all.log file.  Do you have any idea what might be causing this problem?

Thanks,
Mike

On Thu, Mar 18, 2010 at 2:54 PM, Sita Kakunoori <sita@nmr.mgh.harvard.edu> wrote:

Hi Mike,

I don't think the motion artifact could've been causing this error.
It's probably a good idea to fix the talairach if you think it's off because if you are reporting the talairach coordinates, you would want the talairach transform to be reasonably accurate.


Sita.


On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Sita,

Running it with the -no-wsgcaatlas seems to do the trick as far as avoiding
a segmentation fault.  The T1 looks like it has a some motion
artifact--might that be causing problems?  I checked the Talairach transform
and it looks generally alright, although I think it could be improved with
some tweaking.  It passed the automatic failure detection each time I ran
recon-all, though.  Would you recommend trying to improve the transform so
that things down the line run more smoothly?

Best,
Mike



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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