Re: [Freesurfer] Error messages and empty surf files

Hi Bruce,

The T1 images are oriented correctly, but the values are messed up somehow--I'm not sure why. I've attached a screenshot with the problem subject on the left and a normal subject on the right. I've also attached the talairach_with_skull.lta file, which looks normal. Is it possible that recon-all is messing up prior to the watershed?

Thanks!

On Fri, Mar 15, 2013 at 12:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

it seems like the watershed failed and nothing got created after that. You need to track down why. Usually it's either the talaraich that failed or the volume is oriented incorrectly. Can you bring the T1.mgz up in tkmedit and confirm that the directions it shows are anatomically correct? Then look at the transforms/talairach_with_**skull.lta

On Fri, 15 Mar 2013, Hayley Dorfman wrote:

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.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

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-- Hayley