Bruce,
I had quickly scanned the talairach.xfm, but I have to admit that I'm new to the process and wasn't sure what I was looking for. Here are the recon-all.log and talairach.xfm from this subject. Thank you for all the help!
oakimJ
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, November 10, 2010 7:09 PM To: Joakim Vinberg Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] another recon-all error
Did you check the talairach.xfm? Can you send us the recon-all.log file?
On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" jvinberg@omneuron.com wrote:
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
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