Thanks Bruce for the response. mri_info? do you mean when i converted it from analyze to mgz or when I ran recon-all autorecon2 after inserting it to freesurfer.
On Mon, Nov 28, 2016 at 3:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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
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