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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer