Re: [Freesurfer] Recon-all get stucked without error during processing

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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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