Matt, In v4.0, you can try the option -multistrip, which will attempt eight different parameter settings running mri_watershed and will pick the best one.
Nick > Hello freesurfer gurus. > > Recently I was trying to do a fix on a brain that appeared to have a bad > skull strip. The T1 was fine but the brainmask volume came out almost > totally black, with the surfaces confined to some fuzziness in the corner > (appearing very strange in tkmedit). I attempted to fix the skullstrip by > adjusting the watershed, using version 4 to remain consistent with our > other subjects for whom we did recon1 with version 4 to get better > talairachs. Below is the last part of the log. Any ideas? > > ********************************************************* > The input file is T1.mgz > The output file is brainmask.auto.mgz > If this is incorrect, please exit with CTL-C > > Weighting the input with atlas information before watershed > > *************************WATERSHED************************** > Sorting... > first estimation of the COG coord: x=196 y=119 z=233 r=13 > first estimation of the main basin volume: 10195 voxels > mean intensity too low ! > Modification of the image: intensity*10.67 > first estimation of the COG coord: x=196 y=119 z=233 r=13 > first estimation of the main basin volume: 10195 voxels > mri_watershed Error: > Interpolation problem in the white matter curve analysis > > Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 > i686 i386 GNU/Linux > > recon-all exited with ERRORS at Thu Nov 1 16:25:31 CDT 2007 > _______________________________________________ > 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
