Hi Matthieu

was this ever resolved? If not, you can upload the subject and we will take a look. You could also try messing with the watershed parameters (starting with changing the preflooding height to me more aggressive).

cheers
Bruce

On Thu, 10 Dec 2015, Matthieu Vanhoutte wrote:

Hi Bruce,

Do you have an idea of how to solve this problem of skull stripping (below)
?

Best regards,
Matthieu

2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>:
      Hi Bruce,

In fact T1.mgz is ok, but the skull stripping failed and seemed to
have taken only the jawbone and the neck.

Best regards,
Matthieu

2015-12-09 16:16 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Matthieu

      you need to track backwards and see where the problem
      started. Why is the norm warped? Actaully, it shouldn't be
      warped, although it might be truncated if the skull
      stripping failed.

      cheers
      Bruce
      On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote:

            Hi Bruce,

            Indeed norm.mgz isn't empty but doesn't look
            well (truncated and warped).

            Is this bug fixed in the v6 beta release ?

            If this is the case :
            1) Would you advise me to try on the v6 ?
            2) Should I so relaunch all recon-all process
            on my subjects computed with v5.3  and work
            only with the v6 beta ?

            Best regards,
            Matthieu

            2015-12-09 15:55 GMT+01:00 Bruce Fischl
            <fischl@nmr.mgh.harvard.edu>:
                  Hi Matthieu

                  this might be a bug that is fixed in
            6.0. Can you cehck the input to
                  mri_cc (norm.mgz) and make sure it is
            not empty? In older versions if the
                  skull stripping failed and generated an
            empty
                  norm.mgz/aseg.auto_noCCseg.mgz the
            mri_cc code would hang.

                  cheers
                  Bruce

                  On Wed, 9 Dec 2015,
                  Matthieu Vanhoutte wrote:

                  > Dear FS epxerts,
                  >
                  > I have launched a recon-all process on
            a subject. Unfortunately, I tried two times
            but the process get stucked at
                  the same step
                  > without error.
                  >
                  > Please found the recon-all.log
            associated attached to this mail.
                  >
                  > Thanks in advance for helping !
                  >
                  > Best regards,
                  > Matthieu
                  >
                  >
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