Hi Asim

can you give us a bit more information? Where does the brainmask come from? I believe we should detect the fact that the brainmask.mgz is different than the automatically created one (brainmask.auto.mgz) and use it instead. Note that the recon editing mode in freeview sets erased voxels to "1" instead of "0" so we can keep track of edits. You might want to do something similar in whatever stream you are using.

cheers Bruce

On Fri, 18 Oct 2019, Asim Hassan wrote:

External Email - Use Caution

​Good afternoon,

Is there any other way to incorporate a manually edited brain mask into the recon all process other than through the recon-mode in freeview?

Thanks! Asim Hassan Research Technician II Waugh Lab Division of Pediatric Neurology University of Texas Southwestern Medical Center Phone: 214-645-9259

---

UT Southwestern

Medical Center

The future of medicine, today.