Hello all, I would like to take advantage of the gcut feature to remove dura that gets included in many subjects in my dataset. I am using v5.0.0, but when i enter the command from the wiki: recon-all -skullstrip -clean-bm -gcut -subjid <subjid> , i get an exit recon-all with errors, saying "ERROR: Flag -gcut unrecognized."
Any suggestions, so that I can avoid doing all of these edits manually?
Michael
Hi Michael, With 5.0, gcut is run by default I believe. If you look at the recon-all.log for that subject and search for gcut, you should be able to see if it ran. Allison
On Thu, 7 Apr 2011, Dougherty, Michael wrote:
Hello all, I would like to take advantage of the gcut feature to remove dura that gets included in many subjects in my dataset. I am using v5.0.0, but when i enter the command from the wiki: recon-all -skullstrip -clean-bm -gcut -subjid <subjid> , i get an exit recon-all with errors, saying "ERROR: Flag -gcut unrecognized."
Any suggestions, so that I can avoid doing all of these edits manually?
Michael
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Allison Stevens -
Dougherty, Michael