what is the output of mri_info on your new brainmask.mgz and on say the orig.mgz? You may need to conform you brainmask

On Mon, 28 Nov 2016, miracle ozzoude wrote:

Hello Freesurfer, I ran recon-all -autorecon 1 -s subjID on  T1 (T1_nii) image and after
that, I replaced the skull stripped volume generated from FS with the skull stripped
volume from lesion explorer ( using mri_convert in_type analyze  in_orientation LAS
out-type img out_orientation LAS mgz; cp folder/brainmask.mgz
folder/subjID/mri/brainmask.mgz). Then, I ran recon-all -autorecon2 -autorecon2 -s
subjID. My recon-all is stucked at 

CORRECTION DEFECT 0 (vertices=49378, convex hull=3422, v0 =0)
XL defect detected....

Please how do I resolve this problem? 

I am running freesurfer-6 development. I have attached the recon-all/recon-all status to
the email. 

Thank you very much

_______________________________________________
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.