Recon-all get stucked without error during processing

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R: Re: FDR correction

Matthieu Vanhoutte

9 Dec 2015 9 Dec '15

9:32 a.m.

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

Attachments:

attachment.html (text/html — 391 bytes)
recon-all_v1.log (text/x-log — 110.8 KB)

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Bruce Fischl

9 Dec 9 Dec

9:55 a.m.

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

Matthieu Vanhoutte

10:08 a.m.

New subject: Recon-all get stucked without error during processing

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

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.

Bruce Fischl

10:16 a.m.

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 :

Would you advise me to try on the v6 ?

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

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.

Matthieu Vanhoutte

10:25 a.m.

New subject: 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 :

Would you advise me to try on the v6 ?

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

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

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.

Matthieu Vanhoutte

10 Dec 10 Dec

12:43 p.m.

New subject: Recon-all get stucked without error during processing

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 :

Would you advise me to try on the v6 ?

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

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

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.

Bruce Fischl

7 Jan 7 Jan

8:58 a.m.

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


        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.

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

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.

Matthieu Vanhoutte

9:12 a.m.

New subject: Recon-all get stucked without error during processing

Hi Bruce,

This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop.

Changing the watershed parameters could be done in the recon-all command ?

Thanks in advance !

Best regards, Matthieu

2016-01-07 14:58 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

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


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

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

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.

Bruce Fischl

9:21 a.m.

yes, it can be done on the recon-all command line. Check out the help

cheers Bruce On Thu, 7 Jan 2016, Matthieu Vanhoutte wrote:

...

Hi Bruce,

This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop.

Changing the watershed parameters could be done in the recon-all command ?

Thanks in advance !

Best regards, Matthieu

2016-01-07 14:58 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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
                          >
                          >
                   
        _______________________________________________
                    Freesurfer mailing list
                    Freesurfer@nmr.mgh.harvard.edu
                   
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


                    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.




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


        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.

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

Bruce Fischl

10:36 a.m.

try specifying

-no-wsgcaatlas

-no-wsatlas

and rerunning just the skull stripping and see if it fixes things

cheers Bruce On Thu, 7 Jan 2016, Matthieu Vanhoutte wrote:

...

Hi Bruce,

This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop.

Changing the watershed parameters could be done in the recon-all command ?

Thanks in advance !

Best regards, Matthieu

2016-01-07 14:58 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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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Bruce Fischl
Matthieu Vanhoutte