Re: [Freesurfer] skull strip error

Hi Nick,

I should have mentioned that this actually was done with the -no-wsgcaatlas option. The results I sent you were obtained using that command.

Thanks, Dana

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, April 13, 2010 3:09 PM To: Dana W. Moore Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] skull strip error

try adding -nowsgcaatlas to the end of the recon-all command.

n. On Tue, 2010-04-13 at 18:59 +0000, Dana W. Moore wrote:

Hi everyone,

I am using freesurfer version 4.5.0, and have just gotten an error message that I have never received before. The end of the recon-all script is pasted below. what does this mean?

#@# Skull Stripping Mon Apr 5 15:06:52 EDT 2010 /home/fs01/kab2003/FS/133_S_0525/mri

mri_watershed -T1 T1.mgz brainmask.auto.mgz

Mode: T1 normalized volume

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The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C

*************************WATERSHED************************** Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 20676

  Find the largest 110-component...
         heap usage = 128720 Kbytes.
         removing small segments (less than 1 percent of

maxarea).done And identify it as the main brain basin...done Main component: 6553 voxels first estimation of the COG coord: x=124 y=177 z=184 r=110 first estimation of the main basin volume: 5673266 voxels mri_watershed Error: Problem with WM_MIN too small Linux compute-3-14.v4linux 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Apr 5 15:06:54 EDT 2010

Thanks, Dana

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