Hi Bruce,

Thanks for your quick reply! I looked in the mri subfolder for this participant, and many necessary files do not exist for them. These are the only files that were created in their mri subfolder:

mri_nu_correct.mni.log
orig
rawavg.mgz
talairach_with_skull.log
nu.mgz
orig.mgz
T1.mgz
transforms

The talairach transform looks fine (see attached talairach.xfm file), but as I mentioned above, there are no brain.mgz or brainmask.mgz files to check. Additionally, the orig and rawaverage files look like they have proper contrast, but the nu.mgz has a strange "halo" above the brain and the T1.mgz is completely blown out (screenshots attached). The brain is also not in the center of the field of view--could this be affecting skull stripping or the nu file?

Thanks for your help!


On Thu, Mar 14, 2013 at 6:27 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Hayley

the LINE SEARCH messages can be ignored, but not the watershed one. The watershed error means the skull stripping has failed, possibly because of a talairach normalization problem. Have you checked the talairach.xfm and the brain.mgz? That's where I would start

cheers
Bruce



On Thu, 14 Mar 2013, Hayley Dorfman wrote:

Hello,

I'm having trouble with recon-all. For 1 of 49 subjects, it completes with
the following error:

mri_watershed Error: 
 GLOBAL region of the brain empty !

Other errors are found in the log which read:

 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCES

This subject's surf files are also empty.

I found this thread from two years ago mentioning a similar issue, but a
solution was not available:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18863.html

Has there been any progress? I've attached my log file.

Any help is much appreciated!

-Hayley






The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



--
Hayley