Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:
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Hi Douglas,
First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for
the recon-all processing stream. Therefore, I stopped after
-autorecon1 and copied the T1.mgz to brainmask.mgz and
brainmask.auto.mgz and continued processing with -autorecon2 and
-autorecon3. In some subjects (at some timepoints), the recon-all
-autorecon2 -autorecon3 excited with errors, as mentioned below. Now I
have used the following command "recon-all -hires -skullstrip
-no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped
data and it worked fine without errors. I also compared the T1.mgz
from both approaches and they looked identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all
subjects or is there something to consider here?
Best, René
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