Ok thank you Bruce
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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