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