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:[email protected]] Sent: Tuesday, April 13, 2010 3:09 PM To: Dana W. Moore Cc: [email protected] 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 > > ********************************************************* > 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 > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
