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.eduwrote:
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.htmlhttp://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/**compliancelinehttp://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.
