This was the info from mri_convert  when i converted my skull stripped volume to mgz before replacing it with the brainmask from FS 
mri_convert --in_type analyze --in_orientation LAS --out_type mgz --out_orientation LAS brainmask.img brainmask.mgz
cp foldername/subjid/brainmask.mgz foldername/subjd/mri/brainmask.mgz

INFO: could  not find ...mat file for direction cosine info
INFO: use ANALYZE 7.5 hdr -> hist.orient value: 0, transverse unflipped (default 
INFO : if not valid, please provide the information ....... .mat file
analyzeRead() roi_scale 0.00000000
TR= 1000.00, TE = 0.00, TI = 0.00, flip angle  = 0.00
setting input orientation to LAS
i_ras = (-1, 0, 0)
j_ras = (0,1,0)
k_ras = (0,0,1)
setting output orientation to LAS
writing to brainmask.mgz

why do i need the orig.mgz? I thought I only had to replace the brainmask.mgz (from FS) with mine brainmask,mgz( from lesion explorer after i have renamed it to brainmask.mgz). Also, I didn't use the "noskullstrip" flag like you suggested.
Best, 
paul

On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
I mean after you have converted it

On Mon, 28 Nov 2016, miracle ozzoude wrote:

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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