try specifying
-no-wsgcaatlas
or
-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 param
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 :
> Hi Matthieu
>
> was this ever resolved? If
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 :
> 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
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 :
> Hi Matthieu
>
> you need to track backwards and see where the problem started. Why is the
> norm warped? Acta
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 em
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 v
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,
