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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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