Ok thank you Bruce

On Nov 23, 2014 10:37 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

we don't have a binary one, but all voxels in brainmask.mgz that are >5 are in brain and everything <5 is not in brain

cheers
Bruce

On Sun, 23 Nov 2014, Gunjan Gautam wrote:

Thanks,

And what about the binary brain mask? I am able to see only the stripped
volume but need the binary brain mask as well.

Gunjan

On Nov 23, 2014 8:49 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:
      Hi Gunjan

      15 min is about what it is going to take. You could do it faster
      but then the failure rate would go up. We've tuned it to improve
      automaticity and reduce failures quite a bit.

      cheers
      Bruce


      On Sat, 22 Nov 2014, Gunjan Gautam wrote:


            Hi,

            I used recon-all with all and its taking a lot of
            time. My main concern is
            only to get the stripped brain.
            I tried with autorecon1 as well but its also taking
            not less than 15min and
            I need to deal with a huge data. 
            Last stage of autorecon1 is skull stripping which
            takes the NU corrected
            input (as it FS works as a pipeline). Is there any
            way to directly get the
            "stripped brain" and its binary mask.

            I also need to ask, which file of the output (name
            with extension) is the
            "binary brain mask" ?

            Best regards,
            Gunjan



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