Sorry to add another!
I ran recon-all on a subject of mine, and have recon-all exit with the error below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is in fact totally empty-definitely not enough values of 110. Is this due to a specific error that I might be able to bypass, or will adding in WM control points fix things?
Thanks in advance!
Joakim
//********************************************************
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010 i686 i686 i386 GNU/Linux
recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010